From 852dae10d21f745c61cbf36227ba0b31e7b45af7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Wed, 21 Aug 2024 19:50:05 +0200 Subject: [PATCH 01/41] snapshot all files contents by default --- tests/default.nf.test | 895 ++++++++++++++++++++++++++++++++++++- tests/default.nf.test.snap | 90 +++- 2 files changed, 956 insertions(+), 29 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index fb4fc2f29..9ad92c2be 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -15,10 +15,457 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot( - UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + path("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt"), + path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt"), + path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt"), + path("${params.outdir}/bbsplit/WT_REP1.stats.txt"), + path("${params.outdir}/bbsplit/WT_REP2.stats.txt") + ).match("bbsplit") }, + { assert snapshot( path("${params.outdir}/custom/out/genome_gfp.fasta"), - path("${params.outdir}/custom/out/genome_gfp.gtf"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip"), + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip") + ).match("fastqc/raw") }, + { assert snapshot( + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip"), + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip") + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt") + ).match("multiqc_report_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report.html"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg") + ).match("multiqc_report_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData"), + path("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt"), + path("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf"), + path("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt"), + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt") + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt"), + path("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log"), + path("${params.outdir}/salmon/WT_REP1/quant.genes.sf"), + path("${params.outdir}/salmon/WT_REP1/quant.sf"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt"), + path("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log"), + path("${params.outdir}/salmon/WT_REP2/quant.genes.sf"), + path("${params.outdir}/salmon/WT_REP2/quant.sf") + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv"), + path("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv"), + path("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds"), + path("${params.outdir}/salmon/salmon.merged.gene_counts.tsv"), + path("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv"), + path("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv"), + path("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds"), path("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv"), + path("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv"), + path("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv"), + path("${params.outdir}/salmon/tx2gene.tsv") + ).match("salmon") }, + { assert snapshot( path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), @@ -28,8 +475,422 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig")).match() - } + path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData"), + path("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf"), + path("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt") + ).match("star_salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf"), + path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf"), + path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf"), + path("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf"), + path("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf"), + path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf"), + path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf"), + path("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf"), + path("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf"), + path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf"), + path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf"), + path("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf"), + path("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf") + ).match("star_salmon/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary") + ).match("star_salmon/featurecounts") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out"), + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out"), + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out"), + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out"), + path("${params.outdir}/star_salmon/log/WT_REP1.Log.out"), + path("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out"), + path("${params.outdir}/star_salmon/log/WT_REP2.Log.out"), + path("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab") + ).match("star_salmon/log") }, + { assert snapshot( + path("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), + path("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), + path("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt"), + path("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), + path("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt") + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt") + ).match("star_salmon/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt"), + path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls") + ).match("star_salmon/rseqc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds"), + path("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds"), + path("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv"), + path("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv") + ).match("star_salmon/salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf") + ).match("star_salmon/stringtie") }, + { assert snapshot( + path("${params.outdir}/star_salmon/tx2gene.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt"), + path("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log"), + path("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam"), + path("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai"), + path("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf"), + path("${params.outdir}/star_salmon/WT_REP1/quant.sf"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt"), + path("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log"), + path("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam"), + path("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai"), + path("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf"), + path("${params.outdir}/star_salmon/WT_REP2/quant.sf") + ).match("star_salmon") }, + { assert snapshot( + path("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt"), + path("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt") + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } ) } } @@ -47,8 +908,32 @@ nextflow_pipeline { then { assertAll( { assert workflow.success }, - { assert snapshot(UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml")).match() } + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_gfp.fasta").name, + file("${params.outdir}/custom/out/genome_gfp.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } ) } } + } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 7371218e8..db3779ee9 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,35 +1,77 @@ { - "Params: default - stub": { + "references": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.3" + "nf-test": "0.9.0", + "nextflow": "24.04.4" }, - "timestamp": "2024-07-12T16:33:33.623985" + "timestamp": "2024-08-21T19:22:22.006847" }, - "Params: default": { + "fastqc/trim": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", - "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", - "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "salmon.merged.transcript_counts.tsv:md5,ff0f5be09ca7a322672c0074ba35da17", - "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466", - "WT_REP1.forward.bigWig:md5,92ad01ddd1dbb7f6d7e2eae23df58c7c", - "WT_REP1.reverse.bigWig:md5,dcac37ef5fff108afd0632388919dcf7", - "WT_REP2.forward.bigWig:md5,d10cbea27b82745b46077191d3ff2820", - "WT_REP2.reverse.bigWig:md5,2b3a15b511efdbc838574200ee2bec0c" + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,be3df48707a8e573984eefc5c14a03d5", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip:md5,83d97092d77748d5041cbb5d4e138543", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html:md5,16162c5f476b57fb7b3ac10f3e016b0e", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip:md5,fff332745d9186d7ea2c01d9b9aa4442", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html:md5,bce21c8b85bcc591723927356d17109c", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip:md5,a005818480609e511fdc516bde8000c9", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html:md5,87ec232cb87031475c24820324421dee", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip:md5,c714ace4a101fa73462f149ef222003e", + "WT_REP1_trimmed_1_val_1_fastqc.html:md5,747c6ed7dbb2ddea2a231b9fd8726c4c", + "WT_REP1_trimmed_1_val_1_fastqc.zip:md5,88e604365901240bb21dd6e8cd803926", + "WT_REP1_trimmed_2_val_2_fastqc.html:md5,3a0f2595881efe2b1b014f731bb03869", + "WT_REP1_trimmed_2_val_2_fastqc.zip:md5,dbef90ece043fd51bdaa52658e9ee12c", + "WT_REP2_trimmed_1_val_1_fastqc.html:md5,bee0baae4f120d669067d2e6824567f6", + "WT_REP2_trimmed_1_val_1_fastqc.zip:md5,bf4a8372297789a3e4f7662368ac74df", + "WT_REP2_trimmed_2_val_2_fastqc.html:md5,4cc6923a6f76d7ad99d6727f66bcd094", + "WT_REP2_trimmed_2_val_2_fastqc.zip:md5,8d0ea8b64a9524a5dfd9ac20de431868" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-21T19:46:35.901089" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", + "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", + "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", + "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", + "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-21T19:46:35.032801" + }, + "fastqc/raw": { + "content": [ + "RAP1_IAA_30M_REP1_raw_1_fastqc.html:md5,b55cd1ea7b117a32c460e1fe6b075929", + "RAP1_IAA_30M_REP1_raw_1_fastqc.zip:md5,295b8bbb4a9b74c4152d578c959d42d6", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html:md5,08f90dff9def052b80348669f501c0cc", + "RAP1_IAA_30M_REP1_raw_2_fastqc.zip:md5,c7ee8233a262dac8a9badea6dc07354a", + "RAP1_UNINDUCED_REP1_raw_fastqc.html:md5,84540e07fa0432f7f74aaa6ceacfa6d7", + 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From 8eb13116950277154d67c562905f26936a7d94d4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 10:22:26 +0200 Subject: [PATCH 02/41] fix MultiQC paths --- tests/default.nf.test | 622 ++++++++++----------- tests/default.nf.test.snap | 1066 ++++++++++++++++++++++++++++++++++-- 2 files changed, 1341 insertions(+), 347 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 9ad92c2be..b1f8664c6 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -62,319 +62,319 @@ nextflow_pipeline { path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip") ).match("fastqc/trim") }, { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt") - ).match("multiqc_report_data") }, + path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_known.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_novel.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_data.json"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_dupradar-section-plot.txt"), + 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"qualimapReport.html:md5,cdb257840fc73606f61573f991fa394d", + "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", + "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-21T19:46:35.355529" + "timestamp": "2024-08-22T10:15:53.418763" } } \ No newline at end of file From 2265facb23a65971ad3afdce87ea86b3cd61b707 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 14:01:41 +0200 Subject: [PATCH 03/41] update test and snapshot --- tests/default.nf.test | 828 ++++++++++++++++++----------------- tests/default.nf.test.snap | 876 ++++++++++++++++++------------------- 2 files changed, 860 insertions(+), 844 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index b1f8664c6..39e74af72 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -27,44 +27,48 @@ nextflow_pipeline { ).match("references") }, { assert snapshot( path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip"), path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip"), path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip"), path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip"), path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip"), path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip"), path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip"), path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip") + // ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name ).match("fastqc/raw") }, { assert snapshot( path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip"), path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip"), path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip"), path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip"), path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip"), path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip"), path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip"), path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip") + // ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_filtered_reads_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_adapter_content_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), @@ -83,49 +87,28 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_known.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_novel.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_data.json"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_dupradar-section-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fail_strand_check_table.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fastqc_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fastqc.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fastqc_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_infer_experiment.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_junction_annotation.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_3.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_pca-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_flagstat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_stats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_software_versions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_sources.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_pca-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_genomic_origin.txt"), @@ -133,109 +116,57 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_rnaseq_genome_results.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance_plot_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_all.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_All_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Known_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Novel_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_distribution_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_dups_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/salmon_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Read_counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-stats-dp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools_alignment_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_data/star_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/star_summary_table.txt") + path("${params.outdir}/multiqc/star_salmon/multiqc_data/star_summary_table.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-stats-dp.txt").name ).match("multiqc_data") }, { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_report.html"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/dupradar-section-plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fail_strand_check_table.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/general_stats_table.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_bam_stat.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_infer_experiment_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_dups_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_clustering-plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_pca-plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-stats-dp.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_clustering-plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_pca-plot.pdf"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_summary_table.pdf"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fail_strand_check_table.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_adapter_content_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_overrepresented_sequences_plot-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png"), @@ -256,20 +187,14 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/general_stats_table.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/picard_deduplication-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_genomic_origin-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_genomic_origin-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_bam_stat.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_infer_experiment_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_inner_distance_plot_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_inner_distance_plot_Percentages.png"), @@ -277,193 +202,275 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_All_Junctions.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_distribution_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_deseq2_clustering-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_deseq2_pca-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-stats-dp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_alignment_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_alignment_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_salmon_deseq2_clustering-plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_salmon_deseq2_pca-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_summary_table.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/dupradar-section-plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fail_strand_check_table.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_adapter_content_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/general_stats_table.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Normalised.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_bam_stat.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_infer_experiment_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Percentages.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_distribution_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_distribution_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_dups_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_deseq2_clustering-plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_deseq2_pca-plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools_alignment_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools_alignment_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-stats-dp.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_alignment_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_alignment_plot-pct.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_salmon_deseq2_clustering-plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_salmon_deseq2_pca-plot.svg"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_summary_table.svg") + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/star_summary_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name ).match("multiqc_plots") }, { assert snapshot( - path("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData"), - path("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt"), - path("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf"), - path("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt"), path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), path("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt") + path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name ).match("salmon/deseq2_qc") }, { assert snapshot( path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf"), - path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf"), - path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf"), path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz"), - path("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json"), - path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt"), - path("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log"), - path("${params.outdir}/salmon/WT_REP1/quant.genes.sf"), - path("${params.outdir}/salmon/WT_REP1/quant.sf"), path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz"), - path("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json"), - path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), - path("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt"), - path("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log"), - path("${params.outdir}/salmon/WT_REP2/quant.genes.sf"), - path("${params.outdir}/salmon/WT_REP2/quant.sf") + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name ).match("salmon_quant") }, { assert snapshot( - path("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv"), - path("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv"), - path("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds"), - path("${params.outdir}/salmon/salmon.merged.gene_counts.tsv"), - path("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv"), - path("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv"), - path("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds"), - path("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv"), - path("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv"), - path("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv"), - path("${params.outdir}/salmon/tx2gene.tsv") + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name ).match("salmon") }, { assert snapshot( path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), @@ -478,44 +485,46 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") ).match("star_salmon/bigwig") }, { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), path("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData"), path("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf"), path("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt") + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), + // PDFs are not stable + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name ).match("star_salmon/deseq2_qc") }, { assert snapshot( - path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf"), - path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf"), - path("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf"), - path("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf"), - path("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf"), path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), - path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf"), - path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf"), - path("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf"), - path("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf"), - path("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf"), path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), - path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf"), - path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf"), - path("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf"), - path("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf"), - path("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf") + // PDFs are not stable + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name ).match("star_salmon/dupradar") }, { assert snapshot( path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), @@ -541,32 +550,34 @@ nextflow_pipeline { ).match("star_salmon/featurecounts") }, { assert snapshot( path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out"), - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out"), - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out"), path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out"), path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out"), - path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out"), path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out"), - path("${params.outdir}/star_salmon/log/WT_REP1.Log.out"), - path("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out"), path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), - path("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out"), - path("${params.outdir}/star_salmon/log/WT_REP2.Log.out"), - path("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out"), - path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab") + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name ).match("star_salmon/log") }, { assert snapshot( - path("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), - path("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), - path("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt"), - path("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt"), - path("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt") + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name ).match("star_salmon/picard_metrics") }, { assert snapshot( path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), @@ -575,7 +586,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), @@ -586,7 +596,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), @@ -597,7 +606,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), @@ -608,7 +616,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), @@ -619,11 +626,16 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt") + path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), + // HTML reports are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name ).match("star_salmon/qualimap") }, { assert snapshot( path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), @@ -636,21 +648,15 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf"), path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r"), path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r"), path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), @@ -666,16 +672,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), @@ -686,26 +682,11 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r"), path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf"), path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), @@ -720,21 +701,54 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls") + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), + // PDFs and R scripts are not stable + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name ).match("star_salmon/rseqc") }, { assert snapshot( - path("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds"), - path("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds"), - path("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv"), - path("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv") + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), @@ -814,79 +828,81 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/tx2gene.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt"), - path("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log"), - path("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam"), - path("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai"), - path("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf"), - path("${params.outdir}/star_salmon/WT_REP1/quant.sf"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), - path("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt"), - path("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log"), - path("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam"), - path("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai"), - path("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf"), - path("${params.outdir}/star_salmon/WT_REP2/quant.sf") + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name ).match("star_salmon") }, { assert snapshot( - path("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt"), - path("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt") + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name ).match("trimgalore") }, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 6d0dda7f6..5b256173a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,38 +1,40 @@ { "star_salmon/log": { "content": [ - "RAP1_IAA_30M_REP1.Log.final.out:md5,e873ef328fcd2a64c4ffa50313e98e86", - "RAP1_IAA_30M_REP1.Log.out:md5,244caf02f5802e7cf0f208f8452ca97b", - "RAP1_IAA_30M_REP1.Log.progress.out:md5,34b47de754d1490619524ad83020d858", + "RAP1_IAA_30M_REP1.Log.final.out:md5,22c161ade4555ec92f6afc1f85c8953d", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", - "RAP1_UNINDUCED_REP1.Log.final.out:md5,d8c69cb442ff579abe35204c29dae9c8", - "RAP1_UNINDUCED_REP1.Log.out:md5,b36f3a695a556a67aa2910ebde685c8e", - "RAP1_UNINDUCED_REP1.Log.progress.out:md5,75d8fcc46808a8e32c0da671c6270132", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", - "RAP1_UNINDUCED_REP2.Log.final.out:md5,fca4f4597e26b27390f0539e164166e0", - "RAP1_UNINDUCED_REP2.Log.out:md5,d6c2b15757df6da5ccaf13d4c0e14826", - "RAP1_UNINDUCED_REP2.Log.progress.out:md5,31e88fa701efc82a517a5fe36bd826a8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", - "WT_REP1.Log.final.out:md5,738609c3eafe8d06dcf42def3bf43757", - "WT_REP1.Log.out:md5,50525baebcc8fa2c9ba44412869c2dd2", - "WT_REP1.Log.progress.out:md5,9e6c30fe848c69b9df5a619a38d099eb", "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", - "WT_REP2.Log.final.out:md5,9591248c7346b20886670c1f543b2f0c", - "WT_REP2.Log.out:md5,fea20c9c6c7ac17d6f6987f23980ef9e", - "WT_REP2.Log.progress.out:md5,9327bf976b53e26da272ef3ed4cf9caa", - "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23" + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:51.896535" + "timestamp": "2024-08-22T13:59:55.286383" }, "multiqc_data": { "content": [ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", "fastqc_adapter_content_plot.txt:md5,483c649e8d33e6dcb322d32e15d706f0", "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", @@ -51,49 +53,28 @@ "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", "fastqc_sequence_length_distribution_plot.txt:md5,94b79b43b2c661a8e51afc174f2f0ad9", - "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", - "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_top_overrepresented_sequences_table-1.txt:md5,fbd6b1f651b8fbe108b05a19e9ba7ca7", - "fastqc_top_overrepresented_sequences_table.txt:md5,a415f85e91e40b3e33495c8966b589e6", - "junction_saturation_known.txt:md5,35764290a46cc101f5aebc5628e3b5ad", - "junction_saturation_novel.txt:md5,ff0cf3556fc4136fe2c94e271221d581", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_data.json:md5,a63261f981181891271a7e5d8926c24d", - "multiqc_dupradar-section-plot.txt:md5,5667eac48bc03174c9c4e83460807ec0", - "multiqc_fail_strand_check_table.txt:md5,b73dd03ea0a10e270b1c7ff8871c38ba", - "multiqc_fastqc_1.txt:md5,b99924f3ab72ce90b5fffaf22a1b31e1", "multiqc_fastqc.txt:md5,b019c39d428dbf17d81c332e012a0bb3", + "multiqc_fastqc_1.txt:md5,b99924f3ab72ce90b5fffaf22a1b31e1", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", "multiqc_general_stats.txt:md5,37844443ce97f0048d011fa62ebf7bb1", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", - "multiqc_rseqc_infer_experiment.txt:md5,03ecee8f93cc95c3552d78e154694566", "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", - "multiqc_salmon_deseq2_clustering-plot_1.txt:md5,6ccabfcdd11d36e140a7d6615c73ae85", - "multiqc_salmon_deseq2_clustering-plot_2.txt:md5,792ce8a58aefbbd10c0f182fcbc37c7a", - "multiqc_salmon_deseq2_clustering-plot_3.txt:md5,3080d13dee6e437084f27937296ede8a", - "multiqc_salmon_deseq2_clustering-plot_4.txt:md5,c750d2fa8d6dc8a2370335a71d2fa637", - "multiqc_salmon_deseq2_clustering-plot.txt:md5,c39fd219828df33259e48aadcdd1997c", - "multiqc_salmon_deseq2_pca-plot.txt:md5,831426c001fe69be0e1ab2bfe32a234b", - "multiqc_salmon.txt:md5,86f2389f9d203be0c7b636d7a1408853", - "multiqc_samtools_flagstat.txt:md5,9fbe907afc102e2e92aeba44acdfb6fe", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_samtools_stats.txt:md5,02da34ce7fcf3a01d1a464ebb3d10e96", - "multiqc_software_versions.txt:md5,bb23b6121e620de2912f7def95e36193", - "multiqc_sources.txt:md5,4d3a3fd6a24246910e08b68d90145d98", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", + "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,e6817b3941a927f2b4a77fb3518cf7e3", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,1c75490fd2daea7224c45013c0f42b50", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,c31a1e6b2433ea398377d732a646da9d", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,c7ff1e0d3420f66a7c4009ea7f97a1b8", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,aa35ef7e0d5f6e035487e452a5b05eef", + "multiqc_star_salmon_deseq2_pca-plot.txt:md5,9ee379d6fcf4a28b4f7fa604e560f6ea", "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", - "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", @@ -101,51 +82,70 @@ "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", + "rseqc_inner_distance.txt:md5,19c55be80264821100f270661ac4937f", "rseqc_inner_distance_plot_Counts.txt:md5,b8116ab4d78349e72a5d2ee3ca22597c", "rseqc_inner_distance_plot_Percentages.txt:md5,2a9506bb04f2b661de081795cff17f46", - "rseqc_inner_distance.txt:md5,19c55be80264821100f270661ac4937f", "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", - "rseqc_junction_saturation_all.txt:md5,6a4af3f0580e7f12fed0b707b33836bc", - "rseqc_junction_saturation_plot_All_Junctions.txt:md5,71396e635a44463438456554d231c1f6", - "rseqc_junction_saturation_plot_Known_Junctions.txt:md5,62bda26d5771dded4e40531b283795ac", - "rseqc_junction_saturation_plot_Novel_Junctions.txt:md5,9b44ddc7d78fb6831ca1a8430647d6ab", "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", - "rseqc_read_dups.txt:md5,e09d49b6587e3022b9f770b088af653f", - "salmon_plot.txt:md5,38a0cb8ab658b2656ae74c997bb3242c", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "samtools-flagstat-dp_Percentage_of_total.txt:md5,5445d34ddda9f5d54e35f779545896ad", - "samtools-flagstat-dp_Read_counts.txt:md5,cccebc8c848d41c3b2191e57cee5f841", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools-stats-dp.txt:md5,acdd095d1fe4b6503052c6ec8b3dc00e", + "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", - "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1" + "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", + "fastqc_top_overrepresented_sequences_table-1.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "junction_saturation_known.txt", + "junction_saturation_novel.txt", + "multiqc_data.json", + "multiqc_dupradar-section-plot.txt", + "multiqc_fail_strand_check_table.txt", + "multiqc_rseqc_infer_experiment.txt", + "multiqc_salmon.txt", + "multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc_salmon_deseq2_pca-plot.txt", + "multiqc_samtools_flagstat.txt", + "multiqc_samtools_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "rseqc_junction_saturation_all.txt", + "rseqc_junction_saturation_plot_All_Junctions.txt", + "rseqc_junction_saturation_plot_Known_Junctions.txt", + "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_dups.txt", + "salmon_plot.txt", + "samtools-flagstat-dp_Percentage_of_total.txt", + "samtools-flagstat-dp_Read_counts.txt", + "samtools-stats-dp.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:44.214366" + "timestamp": "2024-08-22T13:59:53.391706" }, "trimgalore": { "content": [ - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,4855b4458b4602f8f8dc86b77b39e727", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,b1bbedf586c3c1901b9b3ba8db5468ee", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt:md5,fb3cc54f233d4aa310b7c2ba30b3bcf2", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt:md5,5be4089d9252a5244a6ee8c7c59774f7", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt:md5,9189b9864a499b92c2706ff55fd859ed", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt:md5,36dd954d437deabea5ce31ddbf07f689", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt:md5,93282dd039e017bcec0b6e189c0611f6", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt:md5,523747cec397cd468382f43c3b75520c" + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:56.754941" + "timestamp": "2024-08-22T13:59:56.824816" }, "star_salmon/rseqc": { "content": [ @@ -159,21 +159,15 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", - "RAP1_IAA_30M_REP1.inner_distance_plot.pdf:md5,03edca9ca4a5c82c4d758e85d34227e8", - "WT_REP1.inner_distance_plot.pdf:md5,5e3d720803123089e9048f69a1215d42", - "WT_REP2.inner_distance_plot.pdf:md5,e64489934d7e52ed9ad001f69159c0d7", "RAP1_IAA_30M_REP1.inner_distance_plot.r:md5,ff29586a3be60b4a70b588de8f087abf", "WT_REP1.inner_distance_plot.r:md5,b76b8dde3f2eddc17a08ca2938b9544c", "WT_REP2.inner_distance_plot.r:md5,ca997fdf40d4b5170e1af3b29d760a20", "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,0d3b00e36f5afa9c058fb3a99a5d9dcf", "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,002a82a3fb9fe6eb58e2dce854a5922f", - "RAP1_IAA_30M_REP1.inner_distance.txt:md5,31a96bb6a6d02aceb0562ebb494b80a9", "WT_REP1.inner_distance_freq.txt:md5,458a572ad8e604d7a821fc0cfb8c20c0", "WT_REP1.inner_distance_mean.txt:md5,4a5ce24747f921d8296708660a30571c", - "WT_REP1.inner_distance.txt:md5,1a4f5f571b30549c01837d0aa9801030", "WT_REP2.inner_distance_freq.txt:md5,8fb8b3b9bc1684c3948db4857218959e", "WT_REP2.inner_distance_mean.txt:md5,74177bfbb70daf8bdc3557b3253089b8", - "WT_REP2.inner_distance.txt:md5,070a36f01d25e6afa834ff22d074bb6c", "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", @@ -189,16 +183,6 @@ "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", "WT_REP1.junction_annotation.log:md5,93ff20da87153de88c5686588330abd2", "WT_REP2.junction_annotation.log:md5,1b95af725477bbe771ed4e7b7d693729", - "RAP1_IAA_30M_REP1.splice_events.pdf:md5,a03ce50f9cd182cb842f80848127807b", - "RAP1_IAA_30M_REP1.splice_junction.pdf:md5,a371c5d770cf5a84b2f64a9cdb3dc84f", - "RAP1_UNINDUCED_REP1.splice_events.pdf:md5,34419b35e65ee69a0ab1cd190b1517c9", - "RAP1_UNINDUCED_REP1.splice_junction.pdf:md5,ea60c61dcde48b4faad6fe671ea697c2", - "RAP1_UNINDUCED_REP2.splice_events.pdf:md5,cb5befb62ad61b230fc459edd9bb5480", - "RAP1_UNINDUCED_REP2.splice_junction.pdf:md5,722e981a49e361b453cfef11a3ad416f", - "WT_REP1.splice_events.pdf:md5,83867ac6df76b2689beca43d7bf4089b", - "WT_REP1.splice_junction.pdf:md5,71ab425775274e970605893d322ba100", - "WT_REP2.splice_events.pdf:md5,3df00ed7b83a75efe92b0562e04edcf7", - "WT_REP2.splice_junction.pdf:md5,27acdffbdd5d246e61d2f6cf39c10270", "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", @@ -209,26 +193,11 @@ "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", "WT_REP1.junction.xls:md5,02119fa98515474e525ea86ddd1b189c", "WT_REP2.junction.xls:md5,1a3c7d9a4ac9159b87caa1f4ef4b6748", - "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf:md5,0b45f25d2477c739930e5f24bcafb360", - "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf:md5,ebe39da408d1aaaf1f0b125796aebb96", - "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf:md5,1bdd264a8c29533e0ac2b19858fd62f0", - "WT_REP1.junctionSaturation_plot.pdf:md5,ce01ef9d163f4ab7b56f718a05af90a3", - "WT_REP2.junctionSaturation_plot.pdf:md5,7833db28f4d5c33a92aa027a56fb0b1d", - "RAP1_IAA_30M_REP1.junctionSaturation_plot.r:md5,1de3c7e6d31381e042700dfa67c984c9", - "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r:md5,9f2e4d73bd68a913f994ca208a831736", - "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r:md5,a45099f5b04032b9cfddc0d343260408", - "WT_REP1.junctionSaturation_plot.r:md5,800ec0d463ac95d6f95a4b71024ec22f", - "WT_REP2.junctionSaturation_plot.r:md5,79e8aa9b24c95acf3f4e4510ec203200", "RAP1_IAA_30M_REP1.read_distribution.txt:md5,a181a8045a4aaee911e6acd60cc25d43", "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,1d91e11972e9b0a55035f4d9b2fa9b86", "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,ece206e073f3410f6e40d2ff91c9a714", "WT_REP1.read_distribution.txt:md5,7521690f215bf27fe161b8e6d7c38769", "WT_REP2.read_distribution.txt:md5,c11d02cba5674017b90c8372abee3e39", - "RAP1_IAA_30M_REP1.DupRate_plot.pdf:md5,047edaf51e388e7b64da9431a80d1720", - "RAP1_UNINDUCED_REP1.DupRate_plot.pdf:md5,3268f1d58fc349b7f9be6648afae5fcf", - "RAP1_UNINDUCED_REP2.DupRate_plot.pdf:md5,a4536763402899763fe34577270841f2", - "WT_REP1.DupRate_plot.pdf:md5,258166f8211dd416a2cafcda8405cbcf", - "WT_REP2.DupRate_plot.pdf:md5,d0f0d6be71071dcc1e484968a5535107", "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,0505b253ebe3a21cb06a04a08c9313dd", "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,630db79b02077966911b521a1894e1e1", "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,4c7cbbb403a09b1056591772867977bd", @@ -243,13 +212,44 @@ "WT_REP1.pos.DupRate.xls:md5,aba7ea30dc35e376f7655ef298fcaf1c", "WT_REP1.seq.DupRate.xls:md5,44355ee29233ddd150cd9542e807cc1a", "WT_REP2.pos.DupRate.xls:md5,c683b1637e778113bb0a75843ff290af", - "WT_REP2.seq.DupRate.xls:md5,ab100995d906dcd338ec8f7f8a6d3fe0" + "WT_REP2.seq.DupRate.xls:md5,ab100995d906dcd338ec8f7f8a6d3fe0", + "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", + "WT_REP1.inner_distance_plot.pdf", + "WT_REP2.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance.txt", + "WT_REP1.inner_distance.txt", + "WT_REP2.inner_distance.txt", + "RAP1_IAA_30M_REP1.splice_events.pdf", + "RAP1_IAA_30M_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP1.splice_events.pdf", + "RAP1_UNINDUCED_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP2.splice_events.pdf", + "RAP1_UNINDUCED_REP2.splice_junction.pdf", + "WT_REP1.splice_events.pdf", + "WT_REP1.splice_junction.pdf", + "WT_REP2.splice_events.pdf", + "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", + "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", + "WT_REP1.junctionSaturation_plot.pdf", + "WT_REP2.junctionSaturation_plot.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", + "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", + "WT_REP1.junctionSaturation_plot.r", + "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "WT_REP1.DupRate_plot.pdf", + "WT_REP2.DupRate_plot.pdf" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:54.104166" + "timestamp": "2024-08-22T13:59:55.860954" }, "references": { "content": [ @@ -260,27 +260,27 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-21T19:22:22.006847" + "timestamp": "2024-08-22T13:59:53.18077" }, "star_salmon/deseq2_qc": { "content": [ - "deseq2.dds.RData:md5,38df0dcfc302775cb17b42387105271c", - "deseq2.pca.vals.txt:md5,159d70e157d4273cbf7121a06208a536", - "deseq2.plots.pdf:md5,5e63967a1ce08f73897f325c1507fac5", - "deseq2.sample.dists.txt:md5,c27be3cc1cb2f5c6f663dfe7d538eff3", 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"fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:48.388869" + "timestamp": "2024-08-22T13:59:53.950437" }, "star_salmon/qualimap": { "content": [ @@ -1012,7 +1012,6 @@ "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", "Reads Genomic Origin.png:md5,477fbfe923c7d416b507fb488f659ba9", "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", - "qualimapReport.html:md5,5ccd7f9fca3a3a3e4afdf084b86ac807", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", @@ -1023,7 +1022,6 @@ "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", "Reads Genomic Origin.png:md5,e19e85335cf6f64495f4691f15cf39d8", "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", - "qualimapReport.html:md5,b029f48dd0ecab40b5c01130b56e9fdf", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", @@ -1034,7 +1032,6 @@ "Junction Analysis.png:md5,39ac823182971b41faec683b981cfcfa", "Reads Genomic Origin.png:md5,1c0624213e8627aa2496d045117a4fe8", "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", - "qualimapReport.html:md5,e25a408b054ed1c38a841f83afcf91c5", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", @@ -1045,7 +1042,6 @@ "Junction Analysis.png:md5,91f986214d4367ca124d0c1e79ebdf61", "Reads Genomic Origin.png:md5,c99bbcf2882d7ab7a0093157faa69c72", "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e", - "qualimapReport.html:md5,7a7fdb4827c0cd0e913205a722e8f9cd", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", @@ -1056,16 +1052,20 @@ "Junction Analysis.png:md5,147d7341869d7446ae0ad4dd1e3de700", "Reads Genomic Origin.png:md5,93e1f3e32fa60a4dddc4ca696e1347f0", "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", - "qualimapReport.html:md5,cdb257840fc73606f61573f991fa394d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7" + "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T10:15:53.418763" + "timestamp": "2024-08-22T13:59:55.673329" } } \ No newline at end of file From 434a440faf8e295b31d4d432f7e2861ae973e842 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 14:03:51 +0200 Subject: [PATCH 04/41] update MultiQC paths --- tests/default.nf.test | 618 +++++++++++++++++++++--------------------- 1 file changed, 309 insertions(+), 309 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 39e74af72..ea583e618 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -64,319 +64,319 @@ nextflow_pipeline { file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_filtered_reads_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_adapter_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_overrepresented_sequences_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_n_content_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_n_content_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_sequence_quality_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_base_sequence_quality_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_quality_scores_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_per_sequence_quality_scores_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_counts_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_counts_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot-1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_duplication_levels_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_citations.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fastqc.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fastqc_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_general_stats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_read_distribution.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_star_salmon_deseq2_pca-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_deduplication.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/picard_histogram_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_gene_coverage_profile_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_genomic_origin.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_inner_distance_plot_Percentages.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_annotation_junctions_plot_Events.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_dups_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/star_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_data/star_summary_table.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt"), // These files are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table-1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/fastqc_top_overrepresented_sequences_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_known.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/junction_saturation_novel.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_data.json").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_dupradar-section-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_rseqc_infer_experiment.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_salmon_deseq2_pca-plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_flagstat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_samtools_stats.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_software_versions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_all.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/rseqc_read_dups.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/salmon_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Percentage_of_total.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_data/samtools-stats-dp.txt").name + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name ).match("multiqc_data") }, { assert snapshot( - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_filtered_reads_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/dupradar-section-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_adapter_content_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_overrepresented_sequences_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_base_n_content_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_base_n_content_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_base_sequence_quality_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_base_sequence_quality_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_per_sequence_quality_scores_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_counts_plot-1-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_counts_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_counts_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_sequence_length_distribution_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/featurecounts_biotype_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/picard_deduplication-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_gene_coverage_profile_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/qualimap_genomic_origin-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_inner_distance_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_inner_distance_plot_Percentages.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_distribution_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_deseq2_clustering-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_salmon_deseq2_clustering-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_salmon_deseq2_pca-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/dupradar-section-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fail_strand_check_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc-status-check-heatmap.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_adapter_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/general_stats_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/picard_deduplication-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/qualimap_genomic_origin-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_bam_stat.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_infer_experiment_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/rseqc_read_dups_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/salmon_plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools-stats-dp.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-cnt.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/pdf/star_summary_table.pdf").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fail_strand_check_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/fastqc_top_overrepresented_sequences_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_bam_stat.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_deseq2_pca-plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/salmon_plot.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-flagstat-dp_Read_counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/png/star_summary_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/dupradar-section-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fail_strand_check_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc-status-check-heatmap.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_adapter_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_n_content_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/featurecounts_biotype_plot-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/general_stats_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/picard_deduplication-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/qualimap_genomic_origin-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_bam_stat.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_infer_experiment_plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, - 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file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name ).match("multiqc_plots") }, { assert snapshot( From b7c780f2e85b235d26f9e627202a61bffa8b8af2 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 14:08:20 +0200 Subject: [PATCH 05/41] sort files --- tests/default.nf.test | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index ea583e618..af1e671d0 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -219,6 +219,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, @@ -376,17 +377,16 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name ).match("multiqc_plots") }, { assert snapshot( path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt"), path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt"), + path("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), // These files are not stable file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, @@ -657,16 +657,16 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt"), path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), @@ -737,12 +737,12 @@ nextflow_pipeline { ).match("star_salmon/rseqc") }, { assert snapshot( // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, - file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, @@ -825,32 +825,32 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf") ).match("star_salmon/stringtie") }, { assert snapshot( - path("${params.outdir}/star_salmon/tx2gene.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), - path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), // These files are not stable file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, @@ -951,5 +951,4 @@ nextflow_pipeline { ) } } - } From aa1e6a9817a82db86aa34cec047649f651cad11b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 14:59:26 +0200 Subject: [PATCH 06/41] update test and snapshot --- tests/default.nf.test | 34 +++++------ tests/default.nf.test.snap | 122 ++++++++++++++++++------------------- 2 files changed, 78 insertions(+), 78 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index af1e671d0..90fa50f19 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -89,8 +89,8 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), @@ -167,13 +167,8 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), @@ -186,7 +181,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), @@ -205,7 +199,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), @@ -216,8 +209,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -293,6 +284,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, @@ -300,11 +297,14 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, @@ -486,17 +486,17 @@ nextflow_pipeline { ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData"), - path("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt"), path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), - // PDFs are not stable - file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name + // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name ).match("star_salmon/deseq2_qc") }, { assert snapshot( path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), @@ -549,13 +549,13 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary") ).match("star_salmon/featurecounts") }, { assert snapshot( - path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out"), path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5b256173a..4c2bb5438 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -1,12 +1,12 @@ { "star_salmon/log": { "content": [ - "RAP1_IAA_30M_REP1.Log.final.out:md5,22c161ade4555ec92f6afc1f85c8953d", "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.final.out", "RAP1_IAA_30M_REP1.Log.out", "RAP1_IAA_30M_REP1.Log.progress.out", "RAP1_UNINDUCED_REP1.Log.final.out", @@ -26,7 +26,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:55.286383" + "timestamp": "2024-08-22T14:57:58.85709" }, "multiqc_data": { "content": [ @@ -35,13 +35,13 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "fastqc_adapter_content_plot.txt:md5,483c649e8d33e6dcb322d32e15d706f0", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", - "fastqc_per_base_n_content_plot-1.txt:md5,a1d645a6a6e1a5a7fc3b39f23dec0772", - "fastqc_per_base_n_content_plot.txt:md5,ba1172e969a03a6f1aa0c498b27ff4e6", - "fastqc_per_base_sequence_quality_plot-1.txt:md5,591040c632cdf00f6ae281e41aec2d5b", - "fastqc_per_base_sequence_quality_plot.txt:md5,0b442f770310e23ffc945300f2bacb15", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", @@ -52,13 +52,13 @@ "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", - "fastqc_sequence_length_distribution_plot.txt:md5,94b79b43b2c661a8e51afc174f2f0ad9", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", - "multiqc_fastqc.txt:md5,b019c39d428dbf17d81c332e012a0bb3", - "multiqc_fastqc_1.txt:md5,b99924f3ab72ce90b5fffaf22a1b31e1", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_general_stats.txt:md5,37844443ce97f0048d011fa62ebf7bb1", + "multiqc_general_stats.txt:md5,e729536411db0746fa1089a77216fec0", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", @@ -82,9 +82,9 @@ "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_inner_distance.txt:md5,19c55be80264821100f270661ac4937f", - "rseqc_inner_distance_plot_Counts.txt:md5,b8116ab4d78349e72a5d2ee3ca22597c", - "rseqc_inner_distance_plot_Percentages.txt:md5,2a9506bb04f2b661de081795cff17f46", + "rseqc_inner_distance.txt:md5,33a445ddf5841156362e908d62ab2a81", + "rseqc_inner_distance_plot_Counts.txt:md5,04561343fab91ad7e1e285f5816cf740", + "rseqc_inner_distance_plot_Percentages.txt:md5,92f40f2969a02e28a70b94ae78be045a", "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", @@ -128,7 +128,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:53.391706" + "timestamp": "2024-08-22T14:57:57.607534" }, "trimgalore": { "content": [ @@ -160,24 +160,24 @@ "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", "RAP1_IAA_30M_REP1.inner_distance_plot.r:md5,ff29586a3be60b4a70b588de8f087abf", - "WT_REP1.inner_distance_plot.r:md5,b76b8dde3f2eddc17a08ca2938b9544c", + "WT_REP1.inner_distance_plot.r:md5,94fc957e3bb8f361e813249db5e3371e", "WT_REP2.inner_distance_plot.r:md5,ca997fdf40d4b5170e1af3b29d760a20", "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,0d3b00e36f5afa9c058fb3a99a5d9dcf", "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,002a82a3fb9fe6eb58e2dce854a5922f", - "WT_REP1.inner_distance_freq.txt:md5,458a572ad8e604d7a821fc0cfb8c20c0", - "WT_REP1.inner_distance_mean.txt:md5,4a5ce24747f921d8296708660a30571c", + "WT_REP1.inner_distance_freq.txt:md5,2a6ca2a4a50884fa865e96acb1386cc9", + "WT_REP1.inner_distance_mean.txt:md5,f36f6be86cc002953735999a93a40bf1", "WT_REP2.inner_distance_freq.txt:md5,8fb8b3b9bc1684c3948db4857218959e", "WT_REP2.inner_distance_mean.txt:md5,74177bfbb70daf8bdc3557b3253089b8", - "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", - "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", + "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", - "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", + "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", - "WT_REP1.junction.bed:md5,a0082fba0e4222d41fc5e5c6ba6db453", + "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", "WT_REP1.junction.Interact.bed:md5,a989d63b778be8daa2df6ea57ac3fc93", - "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", + "WT_REP1.junction.bed:md5,a0082fba0e4222d41fc5e5c6ba6db453", "WT_REP2.junction.Interact.bed:md5,0da2295d05c6a5de213c2172350ba87e", + "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", @@ -249,7 +249,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:55.860954" + "timestamp": "2024-08-22T14:57:59.277185" }, "references": { "content": [ @@ -265,22 +265,22 @@ "star_salmon/deseq2_qc": { "content": [ "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", - "deseq2.dds.RData:md5,58d3e28f424fd7162a7818aae87de862", - "deseq2.pca.vals.txt:md5,973a1b32565c846f53390ece800a6e7d", - "deseq2.sample.dists.txt:md5,2030e028f47dd7b9c860be53f04ddd59", "RAP1_IAA_30M_REP1.txt:md5,c9edfeadc7fb5111837101a81af1c87e", "RAP1_UNINDUCED_REP1.txt:md5,18a36718e888c138c65f2a6ecd8862a7", "RAP1_UNINDUCED_REP2.txt:md5,6bd573fd119f84464dfca6044fe41704", "WT_REP1.txt:md5,118f0ab1b07ae7f4ef0b0bbdf738770d", "WT_REP2.txt:md5,c23242f9bc76f5528d17d869554c8d2c", "deseq2.size_factors.RData:md5,5fd85441110c2615b08d8f564b88e011", - "deseq2.plots.pdf" + "deseq2.dds.RData", + "deseq2.pca.vals.txt", + "deseq2.plots.pdf", + "deseq2.sample.dists.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:54.650885" + "timestamp": "2024-08-22T14:57:58.5321" }, "star_salmon/featurecounts": { "content": [ @@ -384,12 +384,12 @@ "salmon/deseq2_qc": { "content": [ "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", - "deseq2.size_factors.RData:md5,a9269d6b1c3f4be50c2975f1862d0789", "RAP1_IAA_30M_REP1.txt:md5,070ac8e0dd225793901887863446798d", - "RAP1_UNINDUCED_REP1.txt:md5,49927ec2c47a93d48a3bbc62f6289c14", + "RAP1_UNINDUCED_REP1.txt:md5,d7a80c27e64f8314547c1062adaab174", "RAP1_UNINDUCED_REP2.txt:md5,a9278cb2b25db32f9f6af60ca8789ca8", "WT_REP1.txt:md5,ec8f0bdfaa7bb558c91e0db2679eec8f", "WT_REP2.txt:md5,3761cdcd554d5b696a42fd83f0f4cab7", + "deseq2.size_factors.RData:md5,85580212f39183401f5bb23ef381e6b5", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -399,7 +399,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:53.737741" + "timestamp": "2024-08-22T14:57:58.223719" }, "salmon": { "content": [ @@ -432,13 +432,8 @@ "dupradar-section-plot.png:md5,3ae5e5cb161b7abd878d718bc71b41f6", "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", - "fastqc_adapter_content_plot.png:md5,0597147ec4a40e3f533607b08acd5723", "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", "fastqc_overrepresented_sequences_plot.png:md5,6f5ffbdf1bf61fabe5e028c8bc85de14", - "fastqc_per_base_n_content_plot-1.png:md5,ecd97d681d3b601f67fb9d11558fbd3f", - "fastqc_per_base_n_content_plot.png:md5,273c97d6c60441b143d5e983e3b60f85", - "fastqc_per_base_sequence_quality_plot-1.png:md5,d5acdf12f9c5270a1b20ea310cc5b44b", - "fastqc_per_base_sequence_quality_plot.png:md5,7d0dbf77de4e10750de5ea5fc5487794", "fastqc_per_sequence_gc_content_plot-1_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", "fastqc_per_sequence_gc_content_plot-1_Percentages.png:md5,953929d50c8490029880e205e4db7959", "fastqc_per_sequence_gc_content_plot_Counts.png:md5,01f124545af788fd5cc7bbf41b005e16", @@ -451,7 +446,6 @@ "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "fastqc_sequence_length_distribution_plot.png:md5,21b621b260171f8f2f087624d3c6de02", "featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6", "featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304", "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", @@ -461,8 +455,8 @@ "qualimap_genomic_origin-cnt.png:md5,49c63998f83c3220a35cd4839bf7fecd", "qualimap_genomic_origin-pct.png:md5,ab6697c27cf430782bda984483e708e9", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_inner_distance_plot_Counts.png:md5,edea96936b90ed2d15a694de6eb62b35", - "rseqc_inner_distance_plot_Percentages.png:md5,2766039a2347f2e9c5c93a3dc2941a23", + "rseqc_inner_distance_plot_Counts.png:md5,1adc2a578d1774ab065195a31256df17", + "rseqc_inner_distance_plot_Percentages.png:md5,382ee483b066cfa168e094d3a932c804", "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,1003e4b5012bbddc40badd9e2dfdda8e", "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,676644afc0aee6f63c1299b691b2b93f", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", @@ -470,7 +464,6 @@ "rseqc_read_distribution_plot-cnt.png:md5,7940585c2e998d91a608ac48716c4ab1", "rseqc_read_distribution_plot-pct.png:md5,b6a312b41ed143a7cd8f19a3dd23696d", "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928", - "salmon_deseq2_clustering-plot.png:md5,575a6c1a74e84598aecdbc5c9f3616ab", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", @@ -481,8 +474,7 @@ "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "star_alignment_plot-cnt.png:md5,60df4a4f2ff26bfc6ab4f6f0196a29e2", "star_alignment_plot-pct.png:md5,fefe14d6a715ec0e6df01bf48c781899", - "star_salmon_deseq2_clustering-plot.png:md5,8b12e179ac7bf0a09245835b32fd2f39", - "star_salmon_deseq2_pca-plot.png:md5,6114e63e598a174d00cad94e3f39e145", + "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", "cutadapt_trimmed_sequences_plot_3_Counts.pdf", @@ -556,6 +548,12 @@ "star_salmon_deseq2_pca-plot.pdf", "star_summary_table.pdf", "fail_strand_check_table.png", + "fastqc_adapter_content_plot.png", + "fastqc_per_base_n_content_plot-1.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot-1.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", @@ -563,11 +561,14 @@ "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "star_salmon_deseq2_clustering-plot.png", + "star_salmon_deseq2_pca-plot.png", "star_summary_table.png", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", @@ -640,14 +641,13 @@ "star_alignment_plot-pct.svg", "star_salmon_deseq2_clustering-plot.svg", "star_salmon_deseq2_pca-plot.svg", - "star_summary_table.svg", - "multiqc_report.html" + "star_summary_table.svg" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:53.538727" + "timestamp": "2024-08-22T14:57:57.921685" }, "star_salmon/picard_metrics": { "content": [ @@ -665,12 +665,12 @@ }, "star_salmon/salmon": { "content": [ + "salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon.merged.gene_counts.tsv", "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", "salmon.merged.gene_counts_length_scaled.tsv", "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", "salmon.merged.gene_counts_scaled.tsv", - "salmon.merged.gene_counts.SummarizedExperiment.rds", - "salmon.merged.gene_counts.tsv", "salmon.merged.gene_lengths.tsv", "salmon.merged.gene_tpm.tsv", "salmon.merged.transcript_counts.SummarizedExperiment.rds", @@ -682,7 +682,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:56.046685" + "timestamp": "2024-08-22T14:57:59.602274" }, "fastqc/raw": { "content": [ @@ -758,10 +758,10 @@ "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", - "t_data.ctab:md5,29bd072d125dacd5415b2d52ea6d2dfd", - "WT_REP1.coverage.gtf:md5,5e1e67d78664538151bde6e14df4d0ef", - "WT_REP1.gene.abundance.txt:md5,1c65d6c9fdf938cffbe9cc7e041e5c97", - "WT_REP1.transcripts.gtf:md5,db70f13e0a437833689d4b7190f8d936", + "t_data.ctab:md5,13caaa5e407b1b0bd874395dde0b3005", + "WT_REP1.coverage.gtf:md5,81b17080623c279b1b9ff1f1d353c212", + "WT_REP1.gene.abundance.txt:md5,0a6f85865a0d3c6d1f0d425bf64d3570", + "WT_REP1.transcripts.gtf:md5,b3fc465d263d7c46816f78a3211de4e8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", @@ -775,36 +775,36 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:56.426958" + "timestamp": "2024-08-22T14:57:59.939836" }, "star_salmon": { "content": [ - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", "RAP1_IAA_30M_REP1.markdup.sorted.bam", "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "fld.gz", @@ -850,7 +850,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:56.620139" + "timestamp": "2024-08-22T14:58:00.187909" }, "versions": { "content": [ From 60ca7737fe7feced6633c119e6c5708cd98a35d6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 15:36:52 +0200 Subject: [PATCH 07/41] update test and snapshot --- tests/default.nf.test | 83 ++++++++++++------------- tests/default.nf.test.snap | 122 ++++++++++++++++++------------------- 2 files changed, 103 insertions(+), 102 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 90fa50f19..84952aeef 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -116,9 +116,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), @@ -149,6 +146,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -190,8 +190,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), @@ -294,6 +292,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, @@ -381,17 +381,17 @@ nextflow_pipeline { ).match("multiqc_plots") }, { assert snapshot( path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt"), - path("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), // These files are not stable file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, - file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name ).match("salmon/deseq2_qc") }, { assert snapshot( path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), @@ -648,15 +648,6 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt"), - path("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), @@ -706,9 +697,18 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, @@ -787,42 +787,43 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt"), - path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt"), - path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf"), path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt"), - path("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf"), path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt"), - path("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf") + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name ).match("star_salmon/stringtie") }, { assert snapshot( path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 4c2bb5438..ffbbbfb77 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -58,19 +58,19 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_general_stats.txt:md5,e729536411db0746fa1089a77216fec0", + "multiqc_general_stats.txt:md5,1646098b9a057635ef1fcfeb33189b53", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_star.txt:md5,ae82337a5f847c86e8ffe14e04dfeaee", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,e6817b3941a927f2b4a77fb3518cf7e3", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,1c75490fd2daea7224c45013c0f42b50", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,c31a1e6b2433ea398377d732a646da9d", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,c7ff1e0d3420f66a7c4009ea7f97a1b8", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,aa35ef7e0d5f6e035487e452a5b05eef", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,9ee379d6fcf4a28b4f7fa604e560f6ea", + "multiqc_star.txt:md5,b3dc9dd2d290f12b8835758654a29edd", + "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", + "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -82,9 +82,6 @@ "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_inner_distance.txt:md5,33a445ddf5841156362e908d62ab2a81", - "rseqc_inner_distance_plot_Counts.txt:md5,04561343fab91ad7e1e285f5816cf740", - "rseqc_inner_distance_plot_Percentages.txt:md5,92f40f2969a02e28a70b94ae78be045a", "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", @@ -93,8 +90,8 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,a44811c928719507cee0f98da7492fd1", - "star_summary_table.txt:md5,32aab6812d43f3c850b739eda99990f1", + "star_alignment_plot.txt:md5,77fc30308bc1b75bcf6e99630fc15344", + "star_summary_table.txt:md5,188cd28a8f309eb7c095694d79920eda", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -114,6 +111,9 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "rseqc_inner_distance.txt", + "rseqc_inner_distance_plot_Counts.txt", + "rseqc_inner_distance_plot_Percentages.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -128,7 +128,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:57.607534" + "timestamp": "2024-08-22T15:35:07.389668" }, "trimgalore": { "content": [ @@ -159,15 +159,6 @@ "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", - "RAP1_IAA_30M_REP1.inner_distance_plot.r:md5,ff29586a3be60b4a70b588de8f087abf", - "WT_REP1.inner_distance_plot.r:md5,94fc957e3bb8f361e813249db5e3371e", - "WT_REP2.inner_distance_plot.r:md5,ca997fdf40d4b5170e1af3b29d760a20", - "RAP1_IAA_30M_REP1.inner_distance_freq.txt:md5,0d3b00e36f5afa9c058fb3a99a5d9dcf", - "RAP1_IAA_30M_REP1.inner_distance_mean.txt:md5,002a82a3fb9fe6eb58e2dce854a5922f", - "WT_REP1.inner_distance_freq.txt:md5,2a6ca2a4a50884fa865e96acb1386cc9", - "WT_REP1.inner_distance_mean.txt:md5,f36f6be86cc002953735999a93a40bf1", - "WT_REP2.inner_distance_freq.txt:md5,8fb8b3b9bc1684c3948db4857218959e", - "WT_REP2.inner_distance_mean.txt:md5,74177bfbb70daf8bdc3557b3253089b8", "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", @@ -216,9 +207,18 @@ "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", "WT_REP1.inner_distance_plot.pdf", "WT_REP2.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance_plot.r", + "WT_REP1.inner_distance_plot.r", + "WT_REP2.inner_distance_plot.r", "RAP1_IAA_30M_REP1.inner_distance.txt", + "RAP1_IAA_30M_REP1.inner_distance_freq.txt", + "RAP1_IAA_30M_REP1.inner_distance_mean.txt", "WT_REP1.inner_distance.txt", + "WT_REP1.inner_distance_freq.txt", + "WT_REP1.inner_distance_mean.txt", "WT_REP2.inner_distance.txt", + "WT_REP2.inner_distance_freq.txt", + "WT_REP2.inner_distance_mean.txt", "RAP1_IAA_30M_REP1.splice_events.pdf", "RAP1_IAA_30M_REP1.splice_junction.pdf", "RAP1_UNINDUCED_REP1.splice_events.pdf", @@ -249,7 +249,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:59.277185" + "timestamp": "2024-08-22T15:35:07.931345" }, "references": { "content": [ @@ -280,7 +280,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:58.5321" + "timestamp": "2024-08-22T15:35:07.764873" }, "star_salmon/featurecounts": { "content": [ @@ -384,22 +384,22 @@ "salmon/deseq2_qc": { "content": [ "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", - "RAP1_IAA_30M_REP1.txt:md5,070ac8e0dd225793901887863446798d", - "RAP1_UNINDUCED_REP1.txt:md5,d7a80c27e64f8314547c1062adaab174", - "RAP1_UNINDUCED_REP2.txt:md5,a9278cb2b25db32f9f6af60ca8789ca8", - "WT_REP1.txt:md5,ec8f0bdfaa7bb558c91e0db2679eec8f", - "WT_REP2.txt:md5,3761cdcd554d5b696a42fd83f0f4cab7", - "deseq2.size_factors.RData:md5,85580212f39183401f5bb23ef381e6b5", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", - "deseq2.sample.dists.txt" + "deseq2.sample.dists.txt", + "RAP1_IAA_30M_REP1.txt", + "RAP1_UNINDUCED_REP1.txt", + "RAP1_UNINDUCED_REP2.txt", + "WT_REP1.txt", + "WT_REP2.txt", + "deseq2.size_factors.RData" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:58.223719" + "timestamp": "2024-08-22T15:35:07.630987" }, "salmon": { "content": [ @@ -455,8 +455,6 @@ "qualimap_genomic_origin-cnt.png:md5,49c63998f83c3220a35cd4839bf7fecd", "qualimap_genomic_origin-pct.png:md5,ab6697c27cf430782bda984483e708e9", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_inner_distance_plot_Counts.png:md5,1adc2a578d1774ab065195a31256df17", - "rseqc_inner_distance_plot_Percentages.png:md5,382ee483b066cfa168e094d3a932c804", "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,1003e4b5012bbddc40badd9e2dfdda8e", "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,676644afc0aee6f63c1299b691b2b93f", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", @@ -472,8 +470,8 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", - "star_alignment_plot-cnt.png:md5,60df4a4f2ff26bfc6ab4f6f0196a29e2", - "star_alignment_plot-pct.png:md5,fefe14d6a715ec0e6df01bf48c781899", + "star_alignment_plot-cnt.png:md5,9fd09a2f2ab54160d2add396817109db", + "star_alignment_plot-pct.png:md5,94ddaa0cadd919493440e9b2d225c288", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -558,6 +556,8 @@ "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", "rseqc_bam_stat.png", + "rseqc_inner_distance_plot_Counts.png", + "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -647,7 +647,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:57.921685" + "timestamp": "2024-08-22T15:35:07.505889" }, "star_salmon/picard_metrics": { "content": [ @@ -734,48 +734,48 @@ "e_data.ctab:md5,3f149502efe2a9d4bac98b1dd18c15e7", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,a052ab04070e72cc318fb7680b0764e3", - "t_data.ctab:md5,50ccf0dd1eec29e2c3fc300b4774e63e", - "RAP1_IAA_30M_REP1.coverage.gtf:md5,cc904ea93fdc057ecb0d215d0d36cb2c", - "RAP1_IAA_30M_REP1.gene.abundance.txt:md5,f9d863eb7c592dae0a150bb75e6dfb11", - "RAP1_IAA_30M_REP1.transcripts.gtf:md5,0d4a9f2704df48c1cc551e67d0321217", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", "e_data.ctab:md5,e82329a443b9ff50a86e42aff91bd704", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", - "t_data.ctab:md5,84dd1bc7a05b232810b895e96ed7f904", - "RAP1_UNINDUCED_REP1.coverage.gtf:md5,7999b0d4310300375a75afc0268c6422", - "RAP1_UNINDUCED_REP1.gene.abundance.txt:md5,43d91c4bd7de0dce0bd4c55a107b15f3", - "RAP1_UNINDUCED_REP1.transcripts.gtf:md5,7baec01c88cc5bca52c82c299b6a56c0", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", "e_data.ctab:md5,10e2d00f93f9e74f224bd3c1bfbeb29b", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,525413b70bcf62c24c8f96182e09883e", - "t_data.ctab:md5,851111ca03fe424b6cda8243778a7699", - "RAP1_UNINDUCED_REP2.coverage.gtf:md5,7ee4e626d7866dc4a7f4ca95149d3ca2", - "RAP1_UNINDUCED_REP2.gene.abundance.txt:md5,1b6cd8a16d7b12f4e0b2da9d008799a6", - "RAP1_UNINDUCED_REP2.transcripts.gtf:md5,e88202e890d56ea9f9d7319043e2dc3d", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", "e_data.ctab:md5,9aa371befc36478d7720d3ea275e6f4d", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,907ab2e06346df131cbdb929afc005a8", - "t_data.ctab:md5,13caaa5e407b1b0bd874395dde0b3005", - "WT_REP1.coverage.gtf:md5,81b17080623c279b1b9ff1f1d353c212", - "WT_REP1.gene.abundance.txt:md5,0a6f85865a0d3c6d1f0d425bf64d3570", - "WT_REP1.transcripts.gtf:md5,b3fc465d263d7c46816f78a3211de4e8", "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", "e_data.ctab:md5,b03f3118d1aa58fceadcb3311028e856", "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", "i_data.ctab:md5,041edee3193df311f621c09f4991892b", - "t_data.ctab:md5,27c3984c29befbe71aa569aa34ce0fc3", - "WT_REP2.coverage.gtf:md5,02bb1a3cb3add2ffae40201e78030a5d", - "WT_REP2.gene.abundance.txt:md5,b470d8d9e5b556bcd5605d5f1984178a", - "WT_REP2.transcripts.gtf:md5,65677f9903f752764e8c240f73e30c45" + "t_data.ctab", + "RAP1_IAA_30M_REP1.coverage.gtf", + "RAP1_IAA_30M_REP1.gene.abundance.txt", + "RAP1_IAA_30M_REP1.transcripts.gtf", + "t_data.ctab", + "RAP1_UNINDUCED_REP1.coverage.gtf", + "RAP1_UNINDUCED_REP1.gene.abundance.txt", + "RAP1_UNINDUCED_REP1.transcripts.gtf", + "t_data.ctab", + "RAP1_UNINDUCED_REP2.coverage.gtf", + "RAP1_UNINDUCED_REP2.gene.abundance.txt", + "RAP1_UNINDUCED_REP2.transcripts.gtf", + "t_data.ctab", + "WT_REP1.coverage.gtf", + "WT_REP1.gene.abundance.txt", + "WT_REP1.transcripts.gtf", + "t_data.ctab", + "WT_REP2.coverage.gtf", + "WT_REP2.gene.abundance.txt", + "WT_REP2.transcripts.gtf" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T14:57:59.939836" + "timestamp": "2024-08-22T15:35:08.116582" }, "star_salmon": { "content": [ @@ -927,13 +927,13 @@ "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843" + "WT_REP2.stats.txt:md5,f6df7d4d9a5b553209f31dec2a30f92b" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:53.163717" + "timestamp": "2024-08-22T15:35:07.2382" }, "salmon_quant": { "content": [ From f8b1d3f6acd630a7e793fec10ebdab880645c24b Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 15:52:24 +0200 Subject: [PATCH 08/41] more snapshots --- tests/featurecounts_group_type.nf.test | 53 +++++++++++++- tests/featurecounts_group_type.nf.test.snap | 77 +++++++++++++++++++++ 2 files changed, 129 insertions(+), 1 deletion(-) create mode 100644 tests/featurecounts_group_type.nf.test.snap diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 69de358f5..5e4b02b75 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -13,7 +13,58 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + path("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt"), + path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt"), + path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt"), + path("${params.outdir}/bbsplit/WT_REP1.stats.txt"), + path("${params.outdir}/bbsplit/WT_REP2.stats.txt") + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html"), + path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html"), + path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html"), + // ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html"), + path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html"), + path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html"), + // ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") } + ) } } } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap new file mode 100644 index 000000000..42918d12b --- /dev/null +++ b/tests/featurecounts_group_type.nf.test.snap @@ -0,0 +1,77 @@ +{ + "references": { + "content": [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,b4776accd1bf7206c7ab0f1d84e4721e" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T15:44:10.068551" + }, + "fastqc/trim": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,3823cf549c84bd16c0a5aa42fa4853e7", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html:md5,874a7e78c3ec55eec7b7b70b661a27f2", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html:md5,c9a605d6c5132c0b37ea22437a94d21e", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html:md5,47510573cc288ff174be16704ae8fce8", + "WT_REP1_trimmed_1_val_1_fastqc.html:md5,dd7deefb9d924cd452c0e8a1789907cc", + "WT_REP1_trimmed_2_val_2_fastqc.html:md5,efbadd5f6f79a2be7ee1ca9cdf12c3a2", + "WT_REP2_trimmed_1_val_1_fastqc.html:md5,113b4b6e3aea6d0cbe533a4f67b47b75", + "WT_REP2_trimmed_2_val_2_fastqc.html:md5,10407149a3a88b5be77fe3b2a090e4c6", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.zip" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T15:44:10.142955" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", + "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", + "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", + "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", + "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T15:44:10.05569" + }, + "fastqc/raw": { + "content": [ + "RAP1_IAA_30M_REP1_raw_1_fastqc.html:md5,4d0fd346e2d8b8083ba1d7b70179f735", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html:md5,b4b3096f031a7d7b51cf45800c9df893", + "RAP1_UNINDUCED_REP1_raw_fastqc.html:md5,fc4bf32d182aaf26c3d5d66a2e1e72d9", + "RAP1_UNINDUCED_REP2_raw_fastqc.html:md5,cf53cc7f31f21541212382f832dedd8d", + "WT_REP1_raw_1_fastqc.html:md5,d78401014c733eea1e560af7a60838ed", + "WT_REP1_raw_2_fastqc.html:md5,21f06f45712b298fda165a8a3cf3acde", + "WT_REP2_raw_1_fastqc.html:md5,c41d4f91d622edc9a9027f1c0cef2b63", + "WT_REP2_raw_2_fastqc.html:md5,c9ce8891cb65d72c6cd2df960f02b81c", + "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "WT_REP1_raw_1_fastqc.zip", + "WT_REP1_raw_2_fastqc.zip", + "WT_REP2_raw_1_fastqc.zip", + "WT_REP2_raw_2_fastqc.zip" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T15:44:10.08366" + } +} \ No newline at end of file From c1d2f6a9a3490b0722dc3e84b74312f7c0a98c4f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 15:52:35 +0200 Subject: [PATCH 09/41] update test and snapshot --- tests/default.nf.test | 2 +- tests/default.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 84952aeef..313bc50d0 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -92,7 +92,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), @@ -134,6 +133,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"),name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ffbbbfb77..ead49356c 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -58,7 +58,6 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_general_stats.txt:md5,1646098b9a057635ef1fcfeb33189b53", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", @@ -99,6 +98,7 @@ "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", + "multiqc_general_stats.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", @@ -1068,4 +1068,4 @@ }, "timestamp": "2024-08-22T13:59:55.673329" } -} \ No newline at end of file +} From d03451ea47b37aa483dfd228a98bdba10755fda6 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 15:59:39 +0200 Subject: [PATCH 10/41] update CHANGELOG --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1f38790f7..6eeabcc7c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -115,6 +115,7 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests - [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround +- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests - [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module ### Parameters From c4a3dde5309564d0b679c1ad83b595e8c5289d93 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 16:22:45 +0200 Subject: [PATCH 11/41] update test and snapshot --- tests/default.nf.test | 25 +++++++++++++------------ tests/default.nf.test.snap | 28 ++++++++++++++-------------- 2 files changed, 27 insertions(+), 26 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 313bc50d0..90ee3094d 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -15,11 +15,12 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot( - path("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt"), - path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt"), - path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt"), - path("${params.outdir}/bbsplit/WT_REP1.stats.txt"), - path("${params.outdir}/bbsplit/WT_REP2.stats.txt") + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name ).match("bbsplit") }, { assert snapshot( path("${params.outdir}/custom/out/genome_gfp.fasta"), @@ -97,7 +98,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), @@ -123,8 +123,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -133,7 +131,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, @@ -146,6 +144,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, @@ -157,7 +156,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), @@ -205,8 +206,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -303,6 +302,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ead49356c..32b37a093 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -63,7 +63,6 @@ "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_star.txt:md5,b3dc9dd2d290f12b8835758654a29edd", "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", @@ -89,8 +88,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", - "star_alignment_plot.txt:md5,77fc30308bc1b75bcf6e99630fc15344", - "star_summary_table.txt:md5,188cd28a8f309eb7c095694d79920eda", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -111,6 +108,7 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "multiqc_star.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -122,13 +120,15 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-stats-dp.txt" + "samtools-stats-dp.txt", + "star_alignment_plot.txt", + "star_summary_table.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:35:07.389668" + "timestamp": "2024-08-22T16:18:49.968848" }, "trimgalore": { "content": [ @@ -470,8 +470,6 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", - "star_alignment_plot-cnt.png:md5,9fd09a2f2ab54160d2add396817109db", - "star_alignment_plot-pct.png:md5,94ddaa0cadd919493440e9b2d225c288", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -567,6 +565,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "star_alignment_plot-cnt.png", + "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", "star_salmon_deseq2_pca-plot.png", "star_summary_table.png", @@ -647,7 +647,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:35:07.505889" + "timestamp": "2024-08-22T16:18:50.128016" }, "star_salmon/picard_metrics": { "content": [ @@ -923,17 +923,17 @@ }, "bbsplit": { "content": [ - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP2.stats.txt:md5,f6df7d4d9a5b553209f31dec2a30f92b" + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:35:07.2382" + "timestamp": "2024-08-22T16:18:49.803978" }, "salmon_quant": { "content": [ From e8cd2ac3c1748ecfc97da10041f9e974b4f0d528 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 16:33:37 +0200 Subject: [PATCH 12/41] update test and snapshot --- tests/featurecounts_group_type.nf.test | 58 ++++++++++++++++++--- tests/featurecounts_group_type.nf.test.snap | 53 ++++++++++++++++--- 2 files changed, 99 insertions(+), 12 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 5e4b02b75..3a2adbf32 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -16,11 +16,12 @@ nextflow_pipeline { assertAll( { assert workflow.success }, { assert snapshot( - path("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt"), - path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt"), - path("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt"), - path("${params.outdir}/bbsplit/WT_REP1.stats.txt"), - path("${params.outdir}/bbsplit/WT_REP2.stats.txt") + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name ).match("bbsplit") }, { assert snapshot( path("${params.outdir}/custom/out/genome_gfp.fasta"), @@ -63,7 +64,52 @@ nextflow_pipeline { file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name - ).match("fastqc/trim") } + ).match("fastqc/trim") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --featurecounts_group_type false - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + featurecounts_group_type = false + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_gfp.fasta").name, + file("${params.outdir}/custom/out/genome_gfp.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } ) } } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 42918d12b..286492c28 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -10,6 +10,47 @@ }, "timestamp": "2024-08-22T15:44:10.068551" }, + "versions": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DESEQ2_QC_STAR_SALMON={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T16:30:35.233269" + }, + "Params: --featurecounts_group_type false - stub": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", + "genome_gfp.fasta", + "genome_gfp.gtf", + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "multiqc_report.html", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T16:31:29.50571" + }, "fastqc/trim": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,3823cf549c84bd16c0a5aa42fa4853e7", @@ -37,17 +78,17 @@ }, "bbsplit": { "content": [ - "RAP1_IAA_30M_REP1.stats.txt:md5,a87292c6f7166096166a9015c2e63dac", - "RAP1_UNINDUCED_REP1.stats.txt:md5,781e49024150a8313779c574b58ad035", - "RAP1_UNINDUCED_REP2.stats.txt:md5,e455d0163bf2d988224b0c0092605213", - "WT_REP1.stats.txt:md5,6eab6936804c1157d5e1c61c0562d7de", - "WT_REP2.stats.txt:md5,002ddf6b828d34979652a40f05462843" + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:44:10.05569" + "timestamp": "2024-08-22T16:30:34.908301" }, "fastqc/raw": { "content": [ From 861c084e6b6d171f7717ab182a6edc6cfd3b482f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 16:34:12 +0200 Subject: [PATCH 13/41] revert update CHANGELOG --- CHANGELOG.md | 1 - 1 file changed, 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 6eeabcc7c..1f38790f7 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -115,7 +115,6 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests - [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround -- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests - [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module ### Parameters From 46e75d79bdf5ec3e51c2cc888a8e296223f60485 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 16:52:33 +0200 Subject: [PATCH 14/41] update test and snapshot --- tests/default.nf.test | 12 ++++++------ tests/default.nf.test.snap | 12 ++++++------ 2 files changed, 12 insertions(+), 12 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 90ee3094d..09b48a22b 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -98,12 +98,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), @@ -145,6 +139,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"),name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 32b37a093..e4ed4cac0 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -63,12 +63,6 @@ "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "multiqc_star_salmon_deseq2_clustering-plot.txt:md5,72d5b6d429709160351d875524a50a7c", - "multiqc_star_salmon_deseq2_clustering-plot_1.txt:md5,37a19cbfb14a04455b57b6160d4ef25e", - "multiqc_star_salmon_deseq2_clustering-plot_2.txt:md5,ebad3b29617432485579000fb421958b", - "multiqc_star_salmon_deseq2_clustering-plot_3.txt:md5,0623170a882f18ef18387da6df69a650", - "multiqc_star_salmon_deseq2_clustering-plot_4.txt:md5,ebaa497884793b38eef593d98516ecc9", - "multiqc_star_salmon_deseq2_pca-plot.txt:md5,be897cdf8bba2b37249925f42a3dceae", "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -109,6 +103,12 @@ "multiqc_software_versions.txt", "multiqc_sources.txt", "multiqc_star.txt", + "multiqc_star_salmon_deseq2_clustering-plot.txt", + "multiqc_star_salmon_deseq2_clustering-plot_1.txt", + "multiqc_star_salmon_deseq2_clustering-plot_2.txt", + "multiqc_star_salmon_deseq2_clustering-plot_3.txt", + "multiqc_star_salmon_deseq2_clustering-plot_4.txt", + "multiqc_star_salmon_deseq2_pca-plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", From 162c8b2b8b56126f3dcaec97a28151d870ed0084 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 17:07:42 +0200 Subject: [PATCH 15/41] typo --- tests/default.nf.test | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 09b48a22b..89397e241 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -139,12 +139,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt"),name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt"),name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt"),name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt"),name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt"),name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt"),name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, From 9a040596eebfebac097d099d8753545e9eda55cb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 22 Aug 2024 17:46:14 +0200 Subject: [PATCH 16/41] more snapshots --- tests/featurecounts_group_type.nf.test | 813 +++++++++++++++++ tests/featurecounts_group_type.nf.test.snap | 953 +++++++++++++++++++- 2 files changed, 1748 insertions(+), 18 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 3a2adbf32..47c37085d 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -65,6 +65,819 @@ nextflow_pipeline { file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt"), + path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), + // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name + ).match("star_salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name + ).match("star_salmon/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name + ).match("star_salmon/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), + // HTML reports are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name + ).match("star_salmon/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), + // PDFs and R scripts are not stable + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + ).match("star_salmon/rseqc") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name + ).match("star_salmon/salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name + ).match("star_salmon/stringtie") }, + { assert snapshot( + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name + ).match("star_salmon") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") ).match("versions") } diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 286492c28..cfb5b38d9 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -1,4 +1,255 @@ { + "star_salmon/log": { + "content": [ + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T17:43:26.652121" + }, + "multiqc_data": { + "content": [ + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", + "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", + "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", + "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", + "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", + "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", + "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", + "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", + "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", + "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", + "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", + "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", + "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", + "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", + 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"t_data.ctab", + "WT_REP2.coverage.gtf", + "WT_REP2.gene.abundance.txt", + "WT_REP2.transcripts.gtf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T17:43:26.873868" + }, + "star_salmon": { + "content": [ + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "WT_REP1.markdup.sorted.bam", + "WT_REP1.markdup.sorted.bam.bai", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "WT_REP2.markdup.sorted.bam", + "WT_REP2.markdup.sorted.bam.bai", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T17:43:26.927936" + }, "fastqc/trim": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,3823cf549c84bd16c0a5aa42fa4853e7", @@ -76,6 +851,40 @@ }, "timestamp": "2024-08-22T15:44:10.142955" }, + "star_salmon/dupradar": { + "content": [ + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,2e0d518a450bb57801cdd075d4e9c217", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,96e2f9e1fc5a22a7d468e6fb4a613370", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,28c30ce734d78d53b1c47c3f87414e4b", + "WT_REP1_dupMatrix.txt:md5,b6aa1b99d91f5fa7a94efeed1c496c00", + "WT_REP2_dupMatrix.txt:md5,02236769150436cf31b7339f612119a5", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,c677048855caf5190f29fa5f7137cd79", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,ea1b4323d3bc83759e8a026416bca32b", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,b062f49a5223a3452075062cdd308043", + "WT_REP1_intercept_slope.txt:md5,e7fcac6d125a7ba746a5cba4a1e66aef", + "WT_REP2_intercept_slope.txt:md5,5af16b07a734b73a2c1103b535f9e26e", + "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", + "WT_REP1_duprateExpBoxplot.pdf", + "WT_REP2_duprateExpBoxplot.pdf", + "RAP1_IAA_30M_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP2_expressionHist.pdf", + "WT_REP1_expressionHist.pdf", + "WT_REP2_expressionHist.pdf", + "RAP1_IAA_30M_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", + "WT_REP1_duprateExpDens.pdf", + "WT_REP2_duprateExpDens.pdf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T17:34:58.606096" + }, "bbsplit": { "content": [ "RAP1_IAA_30M_REP1.stats.txt", @@ -90,29 +899,137 @@ }, "timestamp": "2024-08-22T16:30:34.908301" }, - "fastqc/raw": { + "salmon_quant": { "content": [ - "RAP1_IAA_30M_REP1_raw_1_fastqc.html:md5,4d0fd346e2d8b8083ba1d7b70179f735", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html:md5,b4b3096f031a7d7b51cf45800c9df893", - "RAP1_UNINDUCED_REP1_raw_fastqc.html:md5,fc4bf32d182aaf26c3d5d66a2e1e72d9", - "RAP1_UNINDUCED_REP2_raw_fastqc.html:md5,cf53cc7f31f21541212382f832dedd8d", - "WT_REP1_raw_1_fastqc.html:md5,d78401014c733eea1e560af7a60838ed", - "WT_REP1_raw_2_fastqc.html:md5,21f06f45712b298fda165a8a3cf3acde", - "WT_REP2_raw_1_fastqc.html:md5,c41d4f91d622edc9a9027f1c0cef2b63", - "WT_REP2_raw_2_fastqc.html:md5,c9ce8891cb65d72c6cd2df960f02b81c", - "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", - "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", - "RAP1_UNINDUCED_REP1_raw_fastqc.zip", - "RAP1_UNINDUCED_REP2_raw_fastqc.zip", - "WT_REP1_raw_1_fastqc.zip", - "WT_REP1_raw_2_fastqc.zip", - "WT_REP2_raw_1_fastqc.zip", - "WT_REP2_raw_2_fastqc.zip" + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + 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"cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:44:10.08366" + "timestamp": "2024-08-22T17:34:58.29814" + }, + "star_salmon/qualimap": { + "content": [ + "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", + "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", + "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", + "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", + "Reads Genomic Origin.png:md5,477fbfe923c7d416b507fb488f659ba9", + "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", + "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", + "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", + "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", + "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", + "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", + "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", + "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", + "Reads Genomic Origin.png:md5,e19e85335cf6f64495f4691f15cf39d8", + "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", + "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", + "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", + "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", + "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", + "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", + "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", + "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", + "Junction 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"coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", + "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", + "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", + "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6", + "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5", + "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b", + "Junction Analysis.png:md5,147d7341869d7446ae0ad4dd1e3de700", + "Reads Genomic Origin.png:md5,93e1f3e32fa60a4dddc4ca696e1347f0", + "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", + "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", + "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", + "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html", + "qualimapReport.html" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T17:43:26.686713" } } \ No newline at end of file From f1867adaf0cea3f37203feb8cb0f164f9a6d48f0 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 11:30:19 +0200 Subject: [PATCH 17/41] update snapshots --- tests/default.nf.test | 4 +- tests/default.nf.test.snap | 4 +- tests/featurecounts_group_type.nf.test | 4 +- tests/featurecounts_group_type.nf.test.snap | 6 +- tests/hisat2.nf.test | 73 +++++++++++++++++- tests/hisat2.nf.test.snap | 85 +++++++++++++++++++++ 6 files changed, 165 insertions(+), 11 deletions(-) create mode 100644 tests/hisat2.nf.test.snap diff --git a/tests/default.nf.test b/tests/default.nf.test index 89397e241..9252a267b 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -928,8 +928,8 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_gfp.fasta").name, - file("${params.outdir}/custom/out/genome_gfp.gtf").name, + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index e4ed4cac0..0c28f699a 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -353,8 +353,8 @@ "Params: default - stub": { "content": [ "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", - "genome_gfp.fasta", - "genome_gfp.gtf", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", "RAP1_IAA_30M_REP1_raw.zip", "RAP1_UNINDUCED_REP1_raw.html", diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 47c37085d..a61231132 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -901,8 +901,8 @@ nextflow_pipeline { { assert workflow.success }, { assert snapshot( UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), - file("${params.outdir}/custom/out/genome_gfp.fasta").name, - file("${params.outdir}/custom/out/genome_gfp.gtf").name, + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index cfb5b38d9..4e1b81eda 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -674,8 +674,8 @@ "Params: --featurecounts_group_type false - stub": { "content": [ "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", - "genome_gfp.fasta", - "genome_gfp.gtf", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", "RAP1_IAA_30M_REP1_raw.zip", "RAP1_UNINDUCED_REP1_raw.html", @@ -1032,4 +1032,4 @@ }, "timestamp": "2024-08-22T17:43:26.686713" } -} \ No newline at end of file +} diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index c8b55906e..a1cc00b2d 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -13,8 +13,77 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) } } -} + test("Params: --aligner hisat2 - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + aligner = 'hisat2' + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) + } + } +} diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap new file mode 100644 index 000000000..6c4ca1ae4 --- /dev/null +++ b/tests/hisat2.nf.test.snap @@ -0,0 +1,85 @@ +{ + "Params: --aligner hisat2 - stub": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "multiqc_report.html", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T10:32:59.957379" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T10:32:15.607595" + }, + "references": { + "content": [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T10:32:15.597034" + }, + "versions": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, DESEQ2_QC_PSEUDO={r-base=4.0.3, bioconductor-deseq2=1.28.0}, DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T10:32:15.832405" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T10:32:15.589105" + } +} From 8802e2b88d732537f6cf64ff11ba4df4849dc6a4 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 11:53:33 +0200 Subject: [PATCH 18/41] fastqc html are not stable --- tests/default.nf.test | 36 ++++++++++----------- tests/default.nf.test.snap | 32 +++++++++--------- tests/featurecounts_group_type.nf.test | 36 ++++++++++----------- tests/featurecounts_group_type.nf.test.snap | 32 +++++++++--------- 4 files changed, 68 insertions(+), 68 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 9252a267b..8ee881b5d 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -27,41 +27,41 @@ nextflow_pipeline { path("${params.outdir}/custom/out/genome_gfp.gtf") ).match("references") }, { assert snapshot( - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html"), - // ZIPs are not stable + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name ).match("fastqc/raw") }, { assert snapshot( - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html"), - // ZIPs are not stable + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0c28f699a..0a1fbcef5 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -686,21 +686,21 @@ }, "fastqc/raw": { "content": [ - "RAP1_IAA_30M_REP1_raw_1_fastqc.html:md5,4d0fd346e2d8b8083ba1d7b70179f735", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html:md5,b4b3096f031a7d7b51cf45800c9df893", - "RAP1_UNINDUCED_REP1_raw_fastqc.html:md5,fc4bf32d182aaf26c3d5d66a2e1e72d9", - "RAP1_UNINDUCED_REP2_raw_fastqc.html:md5,cf53cc7f31f21541212382f832dedd8d", - "WT_REP1_raw_1_fastqc.html:md5,d78401014c733eea1e560af7a60838ed", - "WT_REP1_raw_2_fastqc.html:md5,21f06f45712b298fda165a8a3cf3acde", - "WT_REP2_raw_1_fastqc.html:md5,c41d4f91d622edc9a9027f1c0cef2b63", - "WT_REP2_raw_2_fastqc.html:md5,c9ce8891cb65d72c6cd2df960f02b81c", + "RAP1_IAA_30M_REP1_raw_1_fastqc.html", "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html", "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_raw_fastqc.html", "RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "RAP1_UNINDUCED_REP2_raw_fastqc.html", "RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "WT_REP1_raw_1_fastqc.html", "WT_REP1_raw_1_fastqc.zip", + "WT_REP1_raw_2_fastqc.html", "WT_REP1_raw_2_fastqc.zip", + "WT_REP2_raw_1_fastqc.html", "WT_REP2_raw_1_fastqc.zip", + "WT_REP2_raw_2_fastqc.html", "WT_REP2_raw_2_fastqc.zip" ], "meta": { @@ -864,21 +864,21 @@ }, "fastqc/trim": { "content": [ - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,3823cf549c84bd16c0a5aa42fa4853e7", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html:md5,874a7e78c3ec55eec7b7b70b661a27f2", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html:md5,c9a605d6c5132c0b37ea22437a94d21e", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html:md5,47510573cc288ff174be16704ae8fce8", - "WT_REP1_trimmed_1_val_1_fastqc.html:md5,dd7deefb9d924cd452c0e8a1789907cc", - "WT_REP1_trimmed_2_val_2_fastqc.html:md5,efbadd5f6f79a2be7ee1ca9cdf12c3a2", - "WT_REP2_trimmed_1_val_1_fastqc.html:md5,113b4b6e3aea6d0cbe533a4f67b47b75", - "WT_REP2_trimmed_2_val_2_fastqc.html:md5,10407149a3a88b5be77fe3b2a090e4c6", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", "WT_REP2_trimmed_2_val_2_fastqc.zip" ], "meta": { diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index a61231132..5ac0a2450 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -28,41 +28,41 @@ nextflow_pipeline { path("${params.outdir}/custom/out/genome_gfp.gtf") ).match("references") }, { assert snapshot( - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html"), - path("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html"), - // ZIPs are not stable + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name ).match("fastqc/raw") }, { assert snapshot( - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html"), - path("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html"), - // ZIPs are not stable + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 4e1b81eda..6533c8a4a 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -619,21 +619,21 @@ }, "fastqc/raw": { "content": [ - "RAP1_IAA_30M_REP1_raw_1_fastqc.html:md5,4d0fd346e2d8b8083ba1d7b70179f735", - "RAP1_IAA_30M_REP1_raw_2_fastqc.html:md5,b4b3096f031a7d7b51cf45800c9df893", - "RAP1_UNINDUCED_REP1_raw_fastqc.html:md5,fc4bf32d182aaf26c3d5d66a2e1e72d9", - "RAP1_UNINDUCED_REP2_raw_fastqc.html:md5,cf53cc7f31f21541212382f832dedd8d", - "WT_REP1_raw_1_fastqc.html:md5,d78401014c733eea1e560af7a60838ed", - "WT_REP1_raw_2_fastqc.html:md5,21f06f45712b298fda165a8a3cf3acde", - "WT_REP2_raw_1_fastqc.html:md5,c41d4f91d622edc9a9027f1c0cef2b63", - "WT_REP2_raw_2_fastqc.html:md5,c9ce8891cb65d72c6cd2df960f02b81c", + "RAP1_IAA_30M_REP1_raw_1_fastqc.html", "RAP1_IAA_30M_REP1_raw_1_fastqc.zip", + "RAP1_IAA_30M_REP1_raw_2_fastqc.html", "RAP1_IAA_30M_REP1_raw_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_raw_fastqc.html", "RAP1_UNINDUCED_REP1_raw_fastqc.zip", + "RAP1_UNINDUCED_REP2_raw_fastqc.html", "RAP1_UNINDUCED_REP2_raw_fastqc.zip", + "WT_REP1_raw_1_fastqc.html", "WT_REP1_raw_1_fastqc.zip", + "WT_REP1_raw_2_fastqc.html", "WT_REP1_raw_2_fastqc.zip", + "WT_REP2_raw_1_fastqc.html", "WT_REP2_raw_1_fastqc.zip", + "WT_REP2_raw_2_fastqc.html", "WT_REP2_raw_2_fastqc.zip" ], "meta": { @@ -828,21 +828,21 @@ }, "fastqc/trim": { "content": [ - "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html:md5,3823cf549c84bd16c0a5aa42fa4853e7", - "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html:md5,874a7e78c3ec55eec7b7b70b661a27f2", - "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html:md5,c9a605d6c5132c0b37ea22437a94d21e", - "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html:md5,47510573cc288ff174be16704ae8fce8", - "WT_REP1_trimmed_1_val_1_fastqc.html:md5,dd7deefb9d924cd452c0e8a1789907cc", - "WT_REP1_trimmed_2_val_2_fastqc.html:md5,efbadd5f6f79a2be7ee1ca9cdf12c3a2", - "WT_REP2_trimmed_1_val_1_fastqc.html:md5,113b4b6e3aea6d0cbe533a4f67b47b75", - "WT_REP2_trimmed_2_val_2_fastqc.html:md5,10407149a3a88b5be77fe3b2a090e4c6", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", "WT_REP2_trimmed_2_val_2_fastqc.zip" ], "meta": { From 85cf31e02d8eeaacc848568aa6b4ee0e10b64b61 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 12:36:24 +0200 Subject: [PATCH 19/41] update tests and snapshots --- tests/default.nf.test | 12 +- tests/default.nf.test.snap | 16 +- tests/featurecounts_group_type.nf.test | 12 +- tests/featurecounts_group_type.nf.test.snap | 16 +- tests/hisat2.nf.test | 449 +++++++++++++++ tests/hisat2.nf.test.snap | 573 +++++++++++++++++++- 6 files changed, 1032 insertions(+), 46 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 8ee881b5d..ca206f24a 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -487,13 +487,13 @@ nextflow_pipeline { ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 0a1fbcef5..7fde00824 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -265,12 +265,12 @@ "star_salmon/deseq2_qc": { "content": [ "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", - "RAP1_IAA_30M_REP1.txt:md5,c9edfeadc7fb5111837101a81af1c87e", - "RAP1_UNINDUCED_REP1.txt:md5,18a36718e888c138c65f2a6ecd8862a7", - "RAP1_UNINDUCED_REP2.txt:md5,6bd573fd119f84464dfca6044fe41704", - "WT_REP1.txt:md5,118f0ab1b07ae7f4ef0b0bbdf738770d", - "WT_REP2.txt:md5,c23242f9bc76f5528d17d869554c8d2c", - "deseq2.size_factors.RData:md5,5fd85441110c2615b08d8f564b88e011", + "RAP1_IAA_30M_REP1.txt", + "RAP1_UNINDUCED_REP1.txt", + "RAP1_UNINDUCED_REP2.txt", + "WT_REP1.txt", + "WT_REP2.txt", + "deseq2.size_factors.RData", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -280,7 +280,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:35:07.764873" + "timestamp": "2024-08-23T12:20:39.105655" }, "star_salmon/featurecounts": { "content": [ @@ -1068,4 +1068,4 @@ }, "timestamp": "2024-08-22T13:59:55.673329" } -} +} \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 5ac0a2450..06c7d3dfe 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -481,13 +481,13 @@ nextflow_pipeline { ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt"), - path("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData"), // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 6533c8a4a..492d5b49c 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -264,12 +264,12 @@ "star_salmon/deseq2_qc": { "content": [ "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676", - "RAP1_IAA_30M_REP1.txt:md5,c9edfeadc7fb5111837101a81af1c87e", - "RAP1_UNINDUCED_REP1.txt:md5,18a36718e888c138c65f2a6ecd8862a7", - "RAP1_UNINDUCED_REP2.txt:md5,6bd573fd119f84464dfca6044fe41704", - "WT_REP1.txt:md5,118f0ab1b07ae7f4ef0b0bbdf738770d", - "WT_REP2.txt:md5,c23242f9bc76f5528d17d869554c8d2c", - "deseq2.size_factors.RData:md5,5fd85441110c2615b08d8f564b88e011", + "RAP1_IAA_30M_REP1.txt", + "RAP1_UNINDUCED_REP1.txt", + "RAP1_UNINDUCED_REP2.txt", + "WT_REP1.txt", + "WT_REP2.txt", + "deseq2.size_factors.RData", "deseq2.dds.RData", "deseq2.pca.vals.txt", "deseq2.plots.pdf", @@ -279,7 +279,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:34:58.515044" + "timestamp": "2024-08-23T12:28:48.071152" }, "star_salmon/samtools_stats": { "content": [ @@ -1032,4 +1032,4 @@ }, "timestamp": "2024-08-22T17:43:26.686713" } -} +} \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index a1cc00b2d..0c296f94e 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -28,6 +28,455 @@ nextflow_pipeline { path("${params.outdir}/custom/out/genome_gfp.gtf") ).match("references") }, { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), + path("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), + path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), + path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), + path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), + path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), + path("${params.outdir}/hisat2/bigwig/WT_REP1.forward.bigWig"), + path("${params.outdir}/hisat2/bigwig/WT_REP1.reverse.bigWig"), + path("${params.outdir}/hisat2/bigwig/WT_REP2.forward.bigWig"), + path("${params.outdir}/hisat2/bigwig/WT_REP2.reverse.bigWig") + ).match("hisat2/bigwig") }, + { assert snapshot( + path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/hisat2/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/hisat2/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/hisat2/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/hisat2/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/hisat2/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/hisat2/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/hisat2/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/hisat2/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/hisat2/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/hisat2/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/hisat2/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name + ).match("hisat2/dupradar") }, + { assert snapshot( + path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), + path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt"), + path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt.summary"), + path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt"), + path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary") + ).match("hisat2/featurecounts") }, + { assert snapshot( + path("${params.outdir}/hisat2/log/RAP1_IAA_30M_REP1.hisat2.summary.log"), + path("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP1.hisat2.summary.log"), + path("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP2.hisat2.summary.log"), + path("${params.outdir}/hisat2/log/WT_REP1.hisat2.summary.log"), + path("${params.outdir}/hisat2/log/WT_REP2.hisat2.summary.log"), + // These files are not stable + file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/hisat2/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam.bai").name + ).match("hisat2") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/hisat2/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/hisat2/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/hisat2/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/hisat2/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("hisat2/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/hisat2/qualimap/WT_REP2/rnaseq_qc_results.txt"), + // HTML reports are not stable + file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/WT_REP2/qualimapReport.html").name + ).match("hisat2/qualimap") }, + { assert snapshot( + path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), + path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), + path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), + path("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP1.bam_stat.txt"), + path("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP2.bam_stat.txt"), + path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), + path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), + path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), + path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), + path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), + path("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP1.read_distribution.txt"), + path("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP2.read_distribution.txt"), + path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), + path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), + path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), + path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), + path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), + path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), + // PDFs and R scripts are not stable + file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + ).match("hisat2/rseqc") }, + { assert snapshot( + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats"), + path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats") + ).match("hisat2/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/hisat2/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/hisat2/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/hisat2/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/hisat2/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/hisat2/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/hisat2/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/hisat2/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/hisat2/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/hisat2/stringtie/WT_REP2.transcripts.gtf").name + ).match("hisat2/stringtie") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 6c4ca1ae4..30dff22c5 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,4 +1,304 @@ { + "hisat2/rseqc": { + "content": [ + "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b38becac2242c9e565453a3147a3679e", + "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,ae7a5e0ec19906b5f9e2fdb397ad14f3", + "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,494fd84c2550aab95335092b9a12b582", + "WT_REP1.bam_stat.txt:md5,ae49a89df9a95984e0dcbde12b4f6c95", + "WT_REP2.bam_stat.txt:md5,3dc7a3e286e4c244b08df72010060696", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1d4348685fa61819ff8076213d0873b3", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,3ee0f64e82f0b1ac16b5f3e2b30b024c", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,3d17628d178e5a3cc9dc03f32614bff7", + "WT_REP1.infer_experiment.txt:md5,13e3c748f5b968455a39eb9fefd87053", + "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", + "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,8b81a9250f08972f06f88bcfab43421f", + "RAP1_IAA_30M_REP1.junction.bed:md5,173eae77a0cd99001ff229c8bb839f6e", + "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,bed2f59ec92d15b5f90f1c2a14787d64", + "RAP1_UNINDUCED_REP1.junction.bed:md5,52a8150e3e4605f94519072fee16449b", + "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,928e134ad0621398ec59b3248f4bb08c", + "RAP1_UNINDUCED_REP2.junction.bed:md5,de5f7324e1e1958713b7460c9881e42e", + "WT_REP1.junction.Interact.bed:md5,ecd57f03d6a5c582c4c6c7ae13c05144", + "WT_REP1.junction.bed:md5,f5a188b82b4b993abf101b046043852c", + "WT_REP2.junction.Interact.bed:md5,a045b8e3f5b7c680272e0d415621fb3d", + "WT_REP2.junction.bed:md5,3d32038159734b9f1c9d366a090127d4", + "RAP1_IAA_30M_REP1.junction_annotation.log:md5,c06db08a16732003984ce0b7f7bf1fe8", + "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,619a128b608946650338ef4eb1261dff", + "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,f9a772dc8395f9266c81d666a56dc0ab", + "WT_REP1.junction_annotation.log:md5,934d6b1d55cb31cbfe183c7f838dc580", + "WT_REP2.junction_annotation.log:md5,02bf2e27dfd72fb89f3689c955dc57ed", + "RAP1_IAA_30M_REP1.junction_plot.r:md5,7d0e8b2937187d6e527ed70027f7b772", + "RAP1_UNINDUCED_REP1.junction_plot.r:md5,fa47ada2b36809228d1b50244e139733", + "RAP1_UNINDUCED_REP2.junction_plot.r:md5,5a9cdf301449dff95c5d5e708e687116", + "WT_REP1.junction_plot.r:md5,4b59b01d12839dcbce41f317e4c08a01", + "WT_REP2.junction_plot.r:md5,5f0daab3e17d4ae765042c6abaa6cff0", + "RAP1_IAA_30M_REP1.junction.xls:md5,98bf3cdbc11ecedc381be4b7ca7554f5", + "RAP1_UNINDUCED_REP1.junction.xls:md5,84f33de4ead9d9c778c1d74d7061f368", + "RAP1_UNINDUCED_REP2.junction.xls:md5,41169042d84d68782bbf41b4cdf5f7fe", + "WT_REP1.junction.xls:md5,dda86a7a53d4832067962356aa9c64b3", + "WT_REP2.junction.xls:md5,eb39b92002a7b2295d15318451e14d39", + "RAP1_IAA_30M_REP1.read_distribution.txt:md5,69f3731ebe31540eb34be1b581c88bdb", + "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,8324ffb159a4e40555e6d088d7aa6e7f", + "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,a658f427236d094aef6e65ea512a2642", + "WT_REP1.read_distribution.txt:md5,4202e7e0b800e897e76a5ce8bdd804d1", + "WT_REP2.read_distribution.txt:md5,b16004cf92f131094bc87c1aa3a9bd73", + "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,449cc929b5c0afb6fe0d3c42aba022b1", + "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,9c733115d61e98bfd05bc4c6b010abdc", + "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,bd3a2f3806ff7d8a4f3a4d8f44ed8d2c", + "WT_REP1.DupRate_plot.r:md5,c0babc40356d96763f8f09a0c0ecf1b7", + "WT_REP2.DupRate_plot.r:md5,d38e55e5f22b2287a8ec2161df9351d7", + "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,0054db74dc0b03e0d322b41c1c89bf9a", + "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,55415fffae3175eb1d36e27c747460ef", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,828df788550bb2cfd139bfb1bf5855a1", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,dd22981ce08bdff7df4e35e5e10c3e27", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,366805c99a2dfa508caf0b2728cae56b", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,dd7b1c9fc2be67beb0bab769666e9a9d", + "WT_REP1.pos.DupRate.xls:md5,925c9a6b036fb3c19d7881700c544ed3", + "WT_REP1.seq.DupRate.xls:md5,68ca73f1471e38d38eb87f9f9a763a97", + "WT_REP2.pos.DupRate.xls:md5,18af139e2465d911039c825a83c547c4", + "WT_REP2.seq.DupRate.xls:md5,4174d14ca585c2109316b48645e479dc", + "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", + "WT_REP1.inner_distance_plot.pdf", + "WT_REP2.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance_plot.r", + "WT_REP1.inner_distance_plot.r", + "WT_REP2.inner_distance_plot.r", + "RAP1_IAA_30M_REP1.inner_distance.txt", + "RAP1_IAA_30M_REP1.inner_distance_freq.txt", + "RAP1_IAA_30M_REP1.inner_distance_mean.txt", + "WT_REP1.inner_distance.txt", + "WT_REP1.inner_distance_freq.txt", + "WT_REP1.inner_distance_mean.txt", + "WT_REP2.inner_distance.txt", + "WT_REP2.inner_distance_freq.txt", + "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.splice_events.pdf", + "RAP1_IAA_30M_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP1.splice_events.pdf", + "RAP1_UNINDUCED_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP2.splice_events.pdf", + "RAP1_UNINDUCED_REP2.splice_junction.pdf", + "WT_REP1.splice_events.pdf", + "WT_REP1.splice_junction.pdf", + "WT_REP2.splice_events.pdf", + "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", + "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", + "WT_REP1.junctionSaturation_plot.pdf", + "WT_REP2.junctionSaturation_plot.pdf", + "RAP1_IAA_30M_REP1.junctionSaturation_plot.r", + "RAP1_UNINDUCED_REP1.junctionSaturation_plot.r", + "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", + "WT_REP1.junctionSaturation_plot.r", + "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.DupRate_plot.pdf", + "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", + "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", + "WT_REP1.DupRate_plot.pdf", + "WT_REP2.DupRate_plot.pdf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T12:35:11.780439" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + 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DUPRADAR={bioconductor-dupradar=1.32.0}, FASTQC={fastqc=0.12.1}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, HISAT2_ALIGN={hisat2=2.2.1, samtools=1.16.1}, HISAT2_EXTRACTSPLICESITES={hisat2=2.2.1}, MULTIQC_CUSTOM_BIOTYPE={python=3.9.5}, PICARD_MARKDUPLICATES={picard=3.1.1}, QUALIMAP_RNASEQ={qualimap=2.3}, RSEQC_BAMSTAT={rseqc=5.0.2}, RSEQC_INFEREXPERIMENT={rseqc=5.0.2}, RSEQC_INNERDISTANCE={rseqc=5.0.2}, RSEQC_JUNCTIONANNOTATION={rseqc=5.0.2}, RSEQC_JUNCTIONSATURATION={rseqc=5.0.2}, RSEQC_READDISTRIBUTION={rseqc=5.0.2}, RSEQC_READDUPLICATION={rseqc=5.0.2}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, SUBREAD_FEATURECOUNTS={subread=2.0.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_HISAT2_INDEX={untar=1.34}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T10:32:15.832405" + "timestamp": "2024-08-23T12:35:11.679664" + }, + "hisat2/dupradar": { + "content": [ + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8a6bf324a928534cb7ed7a5522aff7d0", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,ae3e70edc98ec8117608f8f608effab9", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,9a5c2672c5817e930c7b884ada8fd92c", + "WT_REP1_dupMatrix.txt:md5,11371da7a087879340c2e7e6842a5d89", + "WT_REP2_dupMatrix.txt:md5,5176c7447c4295f94e2683dd9995cea0", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,1285c70833b46849b726412858736ed7", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a2efe7c3cad6f910d5dc208c2825a245", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,117712525fcbd396f77710f4f4b605d9", + "WT_REP1_intercept_slope.txt:md5,df33cbc6c3cb1c85c0c06cdba7df3873", + "WT_REP2_intercept_slope.txt:md5,38fbb93a419e666bc81020602852b1e2", + "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", + "WT_REP1_duprateExpBoxplot.pdf", + "WT_REP2_duprateExpBoxplot.pdf", + "RAP1_IAA_30M_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP2_expressionHist.pdf", + "WT_REP1_expressionHist.pdf", + "WT_REP2_expressionHist.pdf", + "RAP1_IAA_30M_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", + "WT_REP1_duprateExpDens.pdf", + "WT_REP2_duprateExpDens.pdf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T12:35:11.695025" + }, + "hisat2": { + "content": [ + "RAP1_IAA_30M_REP1.hisat2.summary.log:md5,4273e7a9d0fa8a93ec62e25a70a7e212", + "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678", + "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9", + "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8", + "WT_REP2.hisat2.summary.log:md5,5c0d00bfee4ff563521f6458a13f9476", + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", + "WT_REP1.markdup.sorted.bam", + "WT_REP1.markdup.sorted.bam.bai", + "WT_REP2.markdup.sorted.bam", + "WT_REP2.markdup.sorted.bam.bai" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T12:35:11.72217" + }, + "hisat2/stringtie": { + "content": [ + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,c93ce5b90352398208e3d88c68df45c6", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,fe9d92d1d28e1bc1b223e2ce22b4ef05", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,293d64f70bd8353b822e4fa8a6f082a3", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,d279003d92f7feef9adb31203f84474a", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,ed48a29b77c315cb61a6bf09e68c877d", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,cf2506824949c02e0bfde17a9ed86e61", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,a17c7749a005a89875876eb2d90721d4", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,2e2d760739539fba09cbb666ab95afa1", + "e2t.ctab:md5,54dd6de2daa90e973f47524a738a3d69", + "e_data.ctab:md5,22bdc84c1c4acce9798868e8c7b56004", + "i2t.ctab:md5,dda3d3ccd7d4184d947c654ae73efb7b", + "i_data.ctab:md5,80fe14762a8f7230d516bba37b7275d1", + "t_data.ctab", + "RAP1_IAA_30M_REP1.coverage.gtf", + "RAP1_IAA_30M_REP1.gene.abundance.txt", + "RAP1_IAA_30M_REP1.transcripts.gtf", + "t_data.ctab", + "RAP1_UNINDUCED_REP1.coverage.gtf", + "RAP1_UNINDUCED_REP1.gene.abundance.txt", + "RAP1_UNINDUCED_REP1.transcripts.gtf", + "t_data.ctab", + "RAP1_UNINDUCED_REP2.coverage.gtf", + "RAP1_UNINDUCED_REP2.gene.abundance.txt", + "RAP1_UNINDUCED_REP2.transcripts.gtf", + "t_data.ctab", + "WT_REP1.coverage.gtf", + "WT_REP1.gene.abundance.txt", + "WT_REP1.transcripts.gtf", + "t_data.ctab", + "WT_REP2.coverage.gtf", + "WT_REP2.gene.abundance.txt", + "WT_REP2.transcripts.gtf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T12:35:11.865423" }, "bbsplit": { "content": [ @@ -81,5 +549,74 @@ "nextflow": "24.04.4" }, "timestamp": "2024-08-23T10:32:15.589105" + }, + "salmon_quant": { + "content": [ + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T12:35:11.954394" } -} +} \ No newline at end of file From 12dfaedb3e574c5f7d0d0a2aa367b7a2e1f52b52 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 13:41:30 +0200 Subject: [PATCH 20/41] update tests and snapshots --- tests/default.nf.test | 22 +- tests/default.nf.test.snap | 663 ++++++++++---------- tests/featurecounts_group_type.nf.test | 22 +- tests/featurecounts_group_type.nf.test.snap | 31 +- tests/hisat2.nf.test | 331 +++++++++- tests/hisat2.nf.test.snap | 372 ++++++++++- 6 files changed, 1062 insertions(+), 379 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index ca206f24a..a74bdf491 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -826,6 +826,18 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, { assert snapshot( path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), @@ -854,40 +866,30 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), path("${params.outdir}/star_salmon/tx2gene.tsv"), // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - 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"salmon.merged.gene_counts_length_scaled.tsv", + "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon.merged.gene_counts_scaled.tsv", + "salmon.merged.gene_lengths.tsv", + "salmon.merged.gene_tpm.tsv", + "salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon.merged.transcript_counts.tsv", + "salmon.merged.transcript_lengths.tsv", + "salmon.merged.transcript_tpm.tsv" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T14:57:59.602274" + }, + "star_salmon/bigwig": { + "content": [ + "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8", + "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e", + "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b", + "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737", + "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9", + "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466", + "WT_REP1.forward.bigWig:md5,92ad01ddd1dbb7f6d7e2eae23df58c7c", + "WT_REP1.reverse.bigWig:md5,dcac37ef5fff108afd0632388919dcf7", + "WT_REP2.forward.bigWig:md5,d10cbea27b82745b46077191d3ff2820", + "WT_REP2.reverse.bigWig:md5,2b3a15b511efdbc838574200ee2bec0c" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-22T13:59:54.39954" }, "versions": { "content": [ @@ -935,75 +1013,6 @@ }, "timestamp": "2024-08-22T16:18:49.803978" }, - "salmon_quant": { - "content": [ - "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", - "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", - "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", - "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", - "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", - "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", - "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", - "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", - "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", - "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-22T13:59:53.950437" - }, "star_salmon/qualimap": { "content": [ "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 06c7d3dfe..b70c359ee 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -798,6 +798,18 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, { assert snapshot( path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), @@ -826,40 +838,30 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), path("${params.outdir}/star_salmon/tx2gene.tsv"), // These files are not stable - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, - file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name, file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 492d5b49c..632aa0d17 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -281,6 +281,25 @@ }, "timestamp": "2024-08-23T12:28:48.071152" }, + "star_salmon/markdup": { + "content": [ + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", + "WT_REP1.markdup.sorted.bam", + "WT_REP1.markdup.sorted.bam.bai", + "WT_REP2.markdup.sorted.bam", + "WT_REP2.markdup.sorted.bam.bai" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:34:18.361387" + }, "star_salmon/samtools_stats": { "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", @@ -779,40 +798,30 @@ "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", "fld.gz", "meta_info.json", "flenDist.txt", "salmon_quant.log", "quant.genes.sf", "quant.sf", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", "fld.gz", "meta_info.json", "flenDist.txt", "salmon_quant.log", "quant.genes.sf", "quant.sf", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", "fld.gz", "meta_info.json", "flenDist.txt", "salmon_quant.log", "quant.genes.sf", "quant.sf", - "WT_REP1.markdup.sorted.bam", - "WT_REP1.markdup.sorted.bam.bai", "fld.gz", "meta_info.json", "flenDist.txt", "salmon_quant.log", "quant.genes.sf", "quant.sf", - "WT_REP2.markdup.sorted.bam", - "WT_REP2.markdup.sorted.bam.bai", "fld.gz", "meta_info.json", "flenDist.txt", @@ -824,7 +833,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:43:26.927936" + "timestamp": "2024-08-23T13:34:18.439694" }, "fastqc/trim": { "content": [ diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 0c296f94e..14e396864 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -128,11 +128,6 @@ nextflow_pipeline { path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary") ).match("hisat2/featurecounts") }, { assert snapshot( - path("${params.outdir}/hisat2/log/RAP1_IAA_30M_REP1.hisat2.summary.log"), - path("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP1.hisat2.summary.log"), - path("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP2.hisat2.summary.log"), - path("${params.outdir}/hisat2/log/WT_REP1.hisat2.summary.log"), - path("${params.outdir}/hisat2/log/WT_REP2.hisat2.summary.log"), // These files are not stable file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, file("${params.outdir}/hisat2/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, @@ -144,7 +139,333 @@ nextflow_pipeline { file("${params.outdir}/hisat2/WT_REP1.markdup.sorted.bam.bai").name, file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam").name, file("${params.outdir}/hisat2/WT_REP2.markdup.sorted.bam.bai").name + ).match("hisat2/markdup") }, + { assert snapshot( + file("${params.outdir}/hisat2/log/RAP1_IAA_30M_REP1.hisat2.summary.log").name, + file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP1.hisat2.summary.log").name, + file("${params.outdir}/hisat2/log/RAP1_UNINDUCED_REP2.hisat2.summary.log").name, + file("${params.outdir}/hisat2/log/WT_REP1.hisat2.summary.log").name, + file("${params.outdir}/hisat2/log/WT_REP2.hisat2.summary.log").name ).match("hisat2") }, + { assert snapshot( + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-pct.pdf"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-pct.svg"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name + ).match("multiqc_plots") }, { assert snapshot( // Metrics are not stable file("${params.outdir}/hisat2/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 30dff22c5..b79ca664d 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -120,6 +120,108 @@ }, "timestamp": "2024-08-23T10:32:15.607595" }, + "multiqc_data": { + "content": [ + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "hisat2_pe_plot.txt:md5,ca416ae8b811b11fe4cad79ef583aa3e", + "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", + "multiqc_hisat2.txt:md5,998b80a66a54cf87a571d95d9d6d5798", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "multiqc_citations.txt:md5,da5043f8ab9b5bd51d91ccf3111c655e", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", + "multiqc_picard_dups.txt:md5,71d5bafee1a4916951349018f387f7a0", + "multiqc_rseqc_bam_stat.txt:md5,b259b4e713d5c1b11f61e5f4c2f24660", + "multiqc_rseqc_junction_annotation.txt:md5,7576d6df2e66d72eebc0c2fb9f7fe56e", + "multiqc_rseqc_read_distribution.txt:md5,2254de1c5e6e726f085cb944e7a56442", + "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", + "picard_deduplication.txt:md5,b54a144d4f23ade2221d7ca1af1997f4", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", + "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", + "qualimap_genomic_origin.txt:md5,dd514d2a42da9c4dd1ad4780aa4ac37e", + "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", + "qualimap_rnaseq_genome_results.txt:md5,44d4f08e147731faf8bcc6ace52f00f2", + "rseqc_bam_stat.txt:md5,edfcffb5a74460da3870bec5522b2a3b", + "rseqc_infer_experiment_plot.txt:md5,0556a013129be7d78fac4345fddbe8c5", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,db75ad02153035dea3ffaf58aa68894e", + "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,d233f89c3c69a0dfc2e66d4d5b8c7ea1", + "rseqc_read_distribution_plot.txt:md5,243e8358c7cb5a13d99f715c70c624cb", + "rseqc_read_dups_plot.txt:md5,ed6a2aef667b65f49129c2af874fdbb5", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", + "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", + "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", + "fastqc_top_overrepresented_sequences_table-1.txt", + "fastqc_top_overrepresented_sequences_table.txt", + "junction_saturation_known.txt", + "junction_saturation_novel.txt", + "multiqc_data.json", + "multiqc_dupradar-section-plot.txt", + "multiqc_fail_strand_check_table.txt", + "multiqc_general_stats.txt", + "multiqc_rseqc_infer_experiment.txt", + "multiqc_salmon.txt", + "multiqc_salmon_deseq2_clustering-plot.txt", + "multiqc_salmon_deseq2_clustering-plot_1.txt", + "multiqc_salmon_deseq2_clustering-plot_2.txt", + "multiqc_salmon_deseq2_clustering-plot_3.txt", + "multiqc_salmon_deseq2_clustering-plot_4.txt", + "multiqc_salmon_deseq2_pca-plot.txt", + "multiqc_samtools_flagstat.txt", + "multiqc_samtools_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "multiqc_hisat2_deseq2_clustering-plot.txt", + "multiqc_hisat2_deseq2_clustering-plot_1.txt", + "multiqc_hisat2_deseq2_clustering-plot_2.txt", + "multiqc_hisat2_deseq2_clustering-plot_3.txt", + "multiqc_hisat2_deseq2_clustering-plot_4.txt", + "multiqc_hisat2_deseq2_pca-plot.txt", + "rseqc_inner_distance.txt", + "rseqc_inner_distance_plot_Counts.txt", + "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_saturation_all.txt", + "rseqc_junction_saturation_plot_All_Junctions.txt", + "rseqc_junction_saturation_plot_Known_Junctions.txt", + "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_dups.txt", + "salmon_plot.txt", + "samtools-flagstat-dp_Percentage_of_total.txt", + "samtools-flagstat-dp_Read_counts.txt", + "samtools-stats-dp.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:40:29.874797" + }, "hisat2/picard_metrics": { "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt", @@ -274,6 +376,235 @@ }, "timestamp": "2024-08-23T12:35:11.683972" }, + "multiqc_plots": { + "content": [ + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "hisat2_pe_plot-cnt.pdf:md5,c651fee2195cc5c53a59ecb91be0849b", + "hisat2_pe_plot-pct.pdf:md5,d01bcd3312990174d74ef089d2888ca1", + "hisat2_se_plot-cnt.pdf:md5,5bcc79bb7ed19be777a4299daf1b2cb8", + "hisat2_se_plot-pct.pdf:md5,a57d7425b2e5de0049da1c196a88f07f", + "hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad", + "hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56", + "hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959", + "hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9", + "hisat2_pe_plot-cnt.svg:md5,60288a8893ae236d395970be8787b07a", + "hisat2_pe_plot-pct.svg:md5,186f641284b12305fe134d1ea1c933d4", + "hisat2_se_plot-cnt.svg:md5,335fca14ec90783c11b95da40537cecf", + "hisat2_se_plot-pct.svg:md5,eb97852a1696a3656bd928b2dd9379cf", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "dupradar-section-plot.png:md5,6074ea2315d296094bd10fad3dcc475b", + "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", + 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"fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", + "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", + "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", + "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", + "picard_deduplication-cnt.png:md5,fd520fbb1fda9104eb4d39d42df385d0", + "picard_deduplication-pct.png:md5,dbced4008901ab031eda6d0d96ca038b", + "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", + "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", + "qualimap_genomic_origin-cnt.png:md5,328eb53732bc789d4c9d0aedfc4bcdba", + "qualimap_genomic_origin-pct.png:md5,c5ac55b618d394325f8b0a02463d7ec5", + "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,ac58787f8a0c8fadb4622482cf37f6ae", + "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,bff95e7ddaefdd86188ddb9751e0225f", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,4b91da0c996a436fe52a5b5ce4dee0bf", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,7b304888b33bce8e4c66475711a0a7d1", + "rseqc_read_distribution_plot-cnt.png:md5,07550051821e5b6b2dad0f99c60f2a3e", + "rseqc_read_distribution_plot-pct.png:md5,53cbf7df030a36f7a850580dc7cd6df0", + "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,a56226e705754ce81c7709d40794dd92", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6", + "samtools_alignment_plot-cnt.png:md5,142e06e9daa0fe938f1e9162e1e850a2", + "samtools_alignment_plot-pct.png:md5,bbffb494310e6dff84d9fe7bc99e34fe", + "multiqc_report.html", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "dupradar-section-plot.pdf", + "fail_strand_check_table.pdf", + "fastqc-status-check-heatmap-1.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_adapter_content_plot.pdf", + "fastqc_overrepresented_sequences_plot-1.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot-1.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot-1.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot-1_Counts.pdf", + "fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot-1.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-1-cnt.pdf", + "fastqc_sequence_counts_plot-1-pct.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot-1.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table-1.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "featurecounts_biotype_plot-cnt.pdf", + "featurecounts_biotype_plot-pct.pdf", + "general_stats_table.pdf", + "picard_deduplication-cnt.pdf", + "picard_deduplication-pct.pdf", + "qualimap_gene_coverage_profile_Counts.pdf", + "qualimap_gene_coverage_profile_Normalised.pdf", + "qualimap_genomic_origin-cnt.pdf", + "qualimap_genomic_origin-pct.pdf", + "rseqc_bam_stat.pdf", + "rseqc_infer_experiment_plot.pdf", + "rseqc_inner_distance_plot_Counts.pdf", + "rseqc_inner_distance_plot_Percentages.pdf", + "rseqc_junction_annotation_junctions_plot_Events-cnt.pdf", + "rseqc_junction_annotation_junctions_plot_Events-pct.pdf", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf", + "rseqc_junction_saturation_plot_All_Junctions.pdf", + "rseqc_junction_saturation_plot_Known_Junctions.pdf", + "rseqc_junction_saturation_plot_Novel_Junctions.pdf", + "rseqc_read_distribution_plot-cnt.pdf", + "rseqc_read_distribution_plot-pct.pdf", + "rseqc_read_dups_plot.pdf", + "salmon_deseq2_clustering-plot.pdf", + "salmon_deseq2_pca-plot.pdf", + "salmon_plot.pdf", + "samtools-flagstat-dp_Percentage_of_total.pdf", + "samtools-flagstat-dp_Read_counts.pdf", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf", + "samtools-stats-dp.pdf", + "samtools_alignment_plot-cnt.pdf", + "samtools_alignment_plot-pct.pdf", + "hisat2_deseq2_clustering-plot.pdf", + "hisat2_deseq2_pca-plot.pdf", + "fail_strand_check_table.png", + "fastqc_adapter_content_plot.png", + "fastqc_per_base_n_content_plot-1.png", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot-1.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table-1.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "rseqc_bam_stat.png", + "rseqc_inner_distance_plot_Counts.png", + "rseqc_inner_distance_plot_Percentages.png", + "rseqc_junction_saturation_plot_All_Junctions.png", + "rseqc_junction_saturation_plot_Known_Junctions.png", + "rseqc_junction_saturation_plot_Novel_Junctions.png", + "salmon_deseq2_clustering-plot.png", + "salmon_deseq2_pca-plot.png", + "salmon_plot.png", + "samtools-flagstat-dp_Percentage_of_total.png", + "samtools-flagstat-dp_Read_counts.png", + "samtools-stats-dp.png", + "hisat2_deseq2_clustering-plot.png", + "hisat2_deseq2_pca-plot.png", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "dupradar-section-plot.svg", + "fail_strand_check_table.svg", + "fastqc-status-check-heatmap-1.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_adapter_content_plot.svg", + "fastqc_overrepresented_sequences_plot-1.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot-1.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot-1.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot-1_Counts.svg", + "fastqc_per_sequence_gc_content_plot-1_Percentages.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot-1.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-1-cnt.svg", + "fastqc_sequence_counts_plot-1-pct.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot-1.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table-1.svg", + "fastqc_top_overrepresented_sequences_table.svg", + "featurecounts_biotype_plot-cnt.svg", + "featurecounts_biotype_plot-pct.svg", + "general_stats_table.svg", + "picard_deduplication-cnt.svg", + "picard_deduplication-pct.svg", + "qualimap_gene_coverage_profile_Counts.svg", + "qualimap_gene_coverage_profile_Normalised.svg", + "qualimap_genomic_origin-cnt.svg", + "qualimap_genomic_origin-pct.svg", + "rseqc_bam_stat.svg", + "rseqc_infer_experiment_plot.svg", + "rseqc_inner_distance_plot_Counts.svg", + "rseqc_inner_distance_plot_Percentages.svg", + "rseqc_junction_annotation_junctions_plot_Events-cnt.svg", + "rseqc_junction_annotation_junctions_plot_Events-pct.svg", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.svg", + "rseqc_junction_saturation_plot_All_Junctions.svg", + "rseqc_junction_saturation_plot_Known_Junctions.svg", + "rseqc_junction_saturation_plot_Novel_Junctions.svg", + "rseqc_read_distribution_plot-cnt.svg", + "rseqc_read_distribution_plot-pct.svg", + "rseqc_read_dups_plot.svg", + "salmon_deseq2_clustering-plot.svg", + "salmon_deseq2_pca-plot.svg", + "salmon_plot.svg", + "samtools-flagstat-dp_Percentage_of_total.svg", + "samtools-flagstat-dp_Read_counts.svg", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", + "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg", + "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg", + "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg", + "samtools-stats-dp.svg", + "samtools_alignment_plot-cnt.svg", + "samtools_alignment_plot-pct.svg", + "hisat2_deseq2_clustering-plot.svg", + "hisat2_deseq2_pca-plot.svg" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:40:29.893483" + }, "fastqc/raw": { "content": [ "RAP1_IAA_30M_REP1_raw_1_fastqc.html", @@ -465,27 +796,17 @@ }, "hisat2": { "content": [ - "RAP1_IAA_30M_REP1.hisat2.summary.log:md5,4273e7a9d0fa8a93ec62e25a70a7e212", - "RAP1_UNINDUCED_REP1.hisat2.summary.log:md5,e322e4f7bce12d889a59db517c2ad678", - "RAP1_UNINDUCED_REP2.hisat2.summary.log:md5,3f41605b1fbd4d40983915617f8a91f9", - "WT_REP1.hisat2.summary.log:md5,50cd2a4fe1f041774c572d09156d4ae8", - "WT_REP2.hisat2.summary.log:md5,5c0d00bfee4ff563521f6458a13f9476", - "RAP1_IAA_30M_REP1.markdup.sorted.bam", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", - "WT_REP1.markdup.sorted.bam", - "WT_REP1.markdup.sorted.bam.bai", - "WT_REP2.markdup.sorted.bam", - "WT_REP2.markdup.sorted.bam.bai" + "RAP1_IAA_30M_REP1.hisat2.summary.log", + "RAP1_UNINDUCED_REP1.hisat2.summary.log", + "RAP1_UNINDUCED_REP2.hisat2.summary.log", + "WT_REP1.hisat2.summary.log", + "WT_REP2.hisat2.summary.log" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:35:11.72217" + "timestamp": "2024-08-23T13:40:29.865928" }, "hisat2/stringtie": { "content": [ @@ -618,5 +939,24 @@ "nextflow": "24.04.4" }, "timestamp": "2024-08-23T12:35:11.954394" + }, + "hisat2/markdup": { + "content": [ + "RAP1_IAA_30M_REP1.markdup.sorted.bam", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai", + "WT_REP1.markdup.sorted.bam", + "WT_REP1.markdup.sorted.bam.bai", + "WT_REP2.markdup.sorted.bam", + "WT_REP2.markdup.sorted.bam.bai" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:40:29.820359" } } \ No newline at end of file From 01fadc1c8c7d0ac0e3f7c4fb9185ba3471b88b06 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 14:09:44 +0200 Subject: [PATCH 21/41] update tests and snapshots --- tests/hisat2.nf.test | 24 ++++++++++++------------ tests/hisat2.nf.test.snap | 26 +++++++++++++------------- 2 files changed, 25 insertions(+), 25 deletions(-) diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 14e396864..eb28aab26 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -245,18 +245,10 @@ nextflow_pipeline { ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-pct.pdf"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-pct.svg"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), @@ -336,11 +328,17 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, @@ -370,8 +368,6 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fail_strand_check_table.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, @@ -382,6 +378,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, @@ -394,8 +392,6 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-stats-dp.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, @@ -429,6 +425,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index b79ca664d..962163517 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -379,18 +379,10 @@ "multiqc_plots": { "content": [ "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "hisat2_pe_plot-cnt.pdf:md5,c651fee2195cc5c53a59ecb91be0849b", - "hisat2_pe_plot-pct.pdf:md5,d01bcd3312990174d74ef089d2888ca1", - "hisat2_se_plot-cnt.pdf:md5,5bcc79bb7ed19be777a4299daf1b2cb8", - "hisat2_se_plot-pct.pdf:md5,a57d7425b2e5de0049da1c196a88f07f", "hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad", "hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56", "hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959", "hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9", - "hisat2_pe_plot-cnt.svg:md5,60288a8893ae236d395970be8787b07a", - "hisat2_pe_plot-pct.svg:md5,186f641284b12305fe134d1ea1c933d4", - "hisat2_se_plot-cnt.svg:md5,335fca14ec90783c11b95da40537cecf", - "hisat2_se_plot-pct.svg:md5,eb97852a1696a3656bd928b2dd9379cf", "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", @@ -469,11 +461,17 @@ "featurecounts_biotype_plot-cnt.pdf", "featurecounts_biotype_plot-pct.pdf", "general_stats_table.pdf", + "hisat2_pe_plot-cnt.pdf", + "hisat2_pe_plot-pct.pdf", + "hisat2_se_plot-cnt.pdf", + "hisat2_se_plot-pct.pdf", "picard_deduplication-cnt.pdf", "picard_deduplication-pct.pdf", "qualimap_gene_coverage_profile_Counts.pdf", "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", + "hisat2_deseq2_clustering-plot.pdf", + "hisat2_deseq2_pca-plot.pdf", "qualimap_genomic_origin-pct.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", @@ -503,8 +501,6 @@ "samtools-stats-dp.pdf", "samtools_alignment_plot-cnt.pdf", "samtools_alignment_plot-pct.pdf", - "hisat2_deseq2_clustering-plot.pdf", - "hisat2_deseq2_pca-plot.pdf", "fail_strand_check_table.png", "fastqc_adapter_content_plot.png", "fastqc_per_base_n_content_plot-1.png", @@ -515,6 +511,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "hisat2_deseq2_clustering-plot.png", + "hisat2_deseq2_pca-plot.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", @@ -527,8 +525,6 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", - "hisat2_deseq2_clustering-plot.png", - "hisat2_deseq2_pca-plot.png", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", "cutadapt_trimmed_sequences_plot_3_Counts.svg", @@ -562,6 +558,10 @@ "featurecounts_biotype_plot-cnt.svg", "featurecounts_biotype_plot-pct.svg", "general_stats_table.svg", + "hisat2_pe_plot-cnt.svg", + "hisat2_pe_plot-pct.svg", + "hisat2_se_plot-cnt.svg", + "hisat2_se_plot-pct.svg", "picard_deduplication-cnt.svg", "picard_deduplication-pct.svg", "qualimap_gene_coverage_profile_Counts.svg", @@ -603,7 +603,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T13:40:29.893483" + "timestamp": "2024-08-23T14:08:21.859495" }, "fastqc/raw": { "content": [ From f0f13fe3bd0f5e0b0d0fd3cf3b29d4de3e8d9bc7 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 14:36:09 +0200 Subject: [PATCH 22/41] update tests and snapshots --- tests/hisat2.nf.test | 26 +++++++++++++------------- tests/hisat2.nf.test.snap | 30 +++++++++++++++--------------- 2 files changed, 28 insertions(+), 28 deletions(-) diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index eb28aab26..f9560c7ba 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -153,9 +153,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc-status-check-heatmap.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_adapter_content_plot.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), @@ -206,12 +203,21 @@ nextflow_pipeline { // These files are not stable file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_known.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/junction_saturation_novel.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_data.json").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, @@ -224,12 +230,6 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_1.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_2.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, @@ -245,10 +245,6 @@ nextflow_pipeline { ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), @@ -380,6 +376,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/general_stats_table.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 962163517..4c0e4e4fd 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -127,9 +127,6 @@ "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", - "hisat2_pe_plot.txt:md5,ca416ae8b811b11fe4cad79ef583aa3e", - "hisat2_se_plot.txt:md5,f8cd912353aa55e6e670b72a736b656c", - "multiqc_hisat2.txt:md5,998b80a66a54cf87a571d95d9d6d5798", "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", @@ -179,12 +176,21 @@ "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", + "hisat2_pe_plot.txt", + "hisat2_se_plot.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", "multiqc_data.json", "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_hisat2.txt", + "multiqc_hisat2_deseq2_clustering-plot.txt", + "multiqc_hisat2_deseq2_clustering-plot_1.txt", + "multiqc_hisat2_deseq2_clustering-plot_2.txt", + "multiqc_hisat2_deseq2_clustering-plot_3.txt", + "multiqc_hisat2_deseq2_clustering-plot_4.txt", + "multiqc_hisat2_deseq2_pca-plot.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", @@ -197,12 +203,6 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", - "multiqc_hisat2_deseq2_clustering-plot.txt", - "multiqc_hisat2_deseq2_clustering-plot_1.txt", - "multiqc_hisat2_deseq2_clustering-plot_2.txt", - "multiqc_hisat2_deseq2_clustering-plot_3.txt", - "multiqc_hisat2_deseq2_clustering-plot_4.txt", - "multiqc_hisat2_deseq2_pca-plot.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", @@ -220,7 +220,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T13:40:29.874797" + "timestamp": "2024-08-23T14:34:39.931494" }, "hisat2/picard_metrics": { "content": [ @@ -379,10 +379,6 @@ "multiqc_plots": { "content": [ "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", - "hisat2_pe_plot-cnt.png:md5,1e0841cb32f6aaad84772ff2267b70ad", - "hisat2_pe_plot-pct.png:md5,e201931cd7b31e7227a6273ca1587f56", - "hisat2_se_plot-cnt.png:md5,840937eb5952fa98987a1d2aa8267959", - "hisat2_se_plot-pct.png:md5,51bb5f9ba36dab1ba32fc4e273e865a9", "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", @@ -513,6 +509,10 @@ "general_stats_table.png", "hisat2_deseq2_clustering-plot.png", "hisat2_deseq2_pca-plot.png", + "hisat2_pe_plot-cnt.png", + "hisat2_pe_plot-pct.png", + "hisat2_se_plot-cnt.png", + "hisat2_se_plot-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", @@ -603,7 +603,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T14:08:21.859495" + "timestamp": "2024-08-23T14:34:40.253371" }, "fastqc/raw": { "content": [ From 93cb05eb5f29a6ea744346bfefc2a4da7645d6bf Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 14:47:50 +0200 Subject: [PATCH 23/41] kallisto --- tests/kallisto.nf.test | 44 +++++++++++++++++++++++++++++++++++++ tests/kallisto.nf.test.snap | 33 ++++++++++++++++++++++++++++ 2 files changed, 77 insertions(+) create mode 100644 tests/kallisto.nf.test.snap diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index a6a578a77..bfa0a2cc1 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -18,4 +18,48 @@ nextflow_pipeline { assert workflow.success } } + + test("Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + pseudo_aligner = 'kallisto' + skip_qc = true + skip_alignment = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) + } + } } diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap new file mode 100644 index 000000000..94a97473b --- /dev/null +++ b/tests/kallisto.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "multiqc_report.html", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T14:43:29.078645" + } +} \ No newline at end of file From c64c0337b4ba39cdfce158743dc8159b2665ab87 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 15:36:48 +0200 Subject: [PATCH 24/41] kallisto with snapshots --- tests/kallisto.nf.test | 181 ++++++++++++++++++++++++++-- tests/kallisto.nf.test.snap | 230 ++++++++++++++++++++++++++++++++++-- 2 files changed, 389 insertions(+), 22 deletions(-) diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index bfa0a2cc1..7720fab5e 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -15,7 +15,176 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds"), + path("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds"), + path("${params.outdir}/kallisto/kallisto.merged.gene_counts.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.gene_lengths.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.gene_tpm.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds"), + path("${params.outdir}/kallisto/kallisto.merged.transcript_counts.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.transcript_lengths.tsv"), + path("${params.outdir}/kallisto/kallisto.merged.transcript_tpm.tsv"), + path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.h5"), + path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.tsv"), + path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log"), + path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/run_info.json"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.h5"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.tsv"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/run_info.json"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.h5"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.tsv"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log"), + path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/run_info.json"), + path("${params.outdir}/kallisto/tx2gene.tsv"), + path("${params.outdir}/kallisto/WT_REP1/abundance.h5"), + path("${params.outdir}/kallisto/WT_REP1/abundance.tsv"), + path("${params.outdir}/kallisto/WT_REP1/kallisto_quant.log"), + path("${params.outdir}/kallisto/WT_REP1/run_info.json"), + path("${params.outdir}/kallisto/WT_REP2/abundance.h5"), + path("${params.outdir}/kallisto/WT_REP2/abundance.tsv"), + path("${params.outdir}/kallisto/WT_REP2/kallisto_quant.log"), + path("${params.outdir}/kallisto/WT_REP2/run_info.json") + ).match("kallisto") }, + { assert snapshot( + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/kallisto_alignment.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_kallisto.txt"), + // These files are not stable + file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf"), + path("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg"), + path("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/multiqc_report.html").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) } } @@ -39,16 +208,6 @@ nextflow_pipeline { UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, - file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, file("${params.outdir}/multiqc/multiqc_report.html").name, file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 94a97473b..5fcc98aec 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -1,19 +1,227 @@ { + "multiqc_data": { + "content": [ + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "kallisto_alignment.txt:md5,6f1850f735edb8c199ef69a2aeca746c", + "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_kallisto.txt:md5,30343a3a84fae482f7695355726ef93a", + "fastqc_top_overrepresented_sequences_table.txt", + "multiqc_data.json", + "multiqc_general_stats.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:35:31.485152" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:35:31.545385" + }, + "kallisto": { + "content": [ + "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds:md5,a3fc7ad9b88a6c706d41586ea4bebbd9", + "kallisto.merged.gene_counts_length_scaled.tsv:md5,bb825716e8d3d6b4df2d672c38e8a625", + "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds:md5,3a12e9abc26a8a5a8127425e9220e6ac", + "kallisto.merged.gene_counts_scaled.tsv:md5,ce6ece9365d45cea0a403388af8b583e", + "kallisto.merged.gene_counts.SummarizedExperiment.rds:md5,7bb079c92dd98a7c2c030212bc1affb9", + "kallisto.merged.gene_counts.tsv:md5,bf274bbe1da240633e9179851c916e02", + "kallisto.merged.gene_lengths.tsv:md5,0e55de77f556411d55c69f7e4163722b", + "kallisto.merged.gene_tpm.tsv:md5,164e18ff6f95bb56938fb08d2d40be91", + "kallisto.merged.transcript_counts.SummarizedExperiment.rds:md5,ce6ed19fb07dffa6af29598a0d845d8b", + "kallisto.merged.transcript_counts.tsv:md5,e2a2079e15d2cb31668feee3037ced48", + "kallisto.merged.transcript_lengths.tsv:md5,2c64da3760aba7789c8086d3e0e375bf", + "kallisto.merged.transcript_tpm.tsv:md5,271d646940e3b934c6e0547ea4c8fc2e", + "abundance.h5:md5,d682e51e73620ef44a7ec3285ee64273", + "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", + "kallisto_quant.log:md5,88a4a4c71762af549f1c42308fe80605", + "run_info.json:md5,9d818e3d2ede809baf552274f15ac970", + "abundance.h5:md5,c43fb087de19af669142504061d0e3f7", + "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", + "kallisto_quant.log:md5,b9c4528ce7c00f5f94e7570507d00a51", + "run_info.json:md5,42fc6ba7f61ea1c9fdf986859a9ebf3a", + "abundance.h5:md5,8211dd327e87d33e186373177481f0ab", + "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", + "kallisto_quant.log:md5,8a9605e9d228c9cbec97b0883d909754", + "run_info.json:md5,975d7f1cc482f2a735ab064ac635ae78", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "abundance.h5:md5,94c8aaf349b7c47bc507bf1e84d08b1b", + "abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6", + "kallisto_quant.log:md5,5a7f563172800853c627e8e4f5da6bdc", + "run_info.json:md5,f468d320b4efcdd786ead7826e157017", + "abundance.h5:md5,a988b7e8adffd92cc9b7a096b31f83f7", + "abundance.tsv:md5,780a5d5c6d12b81f4c1865d0b9e125d3", + "kallisto_quant.log:md5,78bf71d8a5b300cc10ed119fdf69c3c0", + "run_info.json:md5,782f358803dca4a54dc7e817a4ba5776" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:35:31.465634" + }, + "references": { + "content": [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:25:12.683541" + }, + "versions": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, KALLISTO_QUANT={kallisto=0.48.0}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:35:31.742801" + }, + "fastqc/trim": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:25:12.695474" + }, + "multiqc_plots": { + "content": [ + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "kallisto_alignment-cnt.pdf:md5,1df1469743dc958991c5680bcad4d06b", + "kallisto_alignment-pct.pdf:md5,310edbb17d863cd91213e54cacc3ff28", + "kallisto_alignment-cnt.png:md5,27547934e07e17907e0f52eac50cc45c", + "kallisto_alignment-pct.png:md5,c34202594e60c3cdc1c713d066e7a381", + "kallisto_alignment-cnt.svg:md5,0112322ad8179e1a41520877a1fc0e73", + "kallisto_alignment-pct.svg:md5,5c7555a00804ef595254d12a7852d12d", + "multiqc_report.html", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "general_stats_table.pdf", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg", + "general_stats_table.svg" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:35:31.50623" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T15:25:12.672876" + }, "Params: --pseudo_aligner kallisto --skip_qc --skip_alignment - stub": { "content": [ "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, KALLISTO_INDEX={kallisto=0.48.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", "multiqc_report.html", "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", @@ -28,6 +236,6 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T14:43:29.078645" + "timestamp": "2024-08-23T15:36:19.174739" } } \ No newline at end of file From 0c296e566bf64f56757639ce1f0f554db267a645 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 15:54:49 +0200 Subject: [PATCH 25/41] kallisto updated snapshots --- tests/kallisto.nf.test | 83 +++++++++++++++++----------------- tests/kallisto.nf.test.snap | 88 ++++++++++++++++++------------------- 2 files changed, 86 insertions(+), 85 deletions(-) diff --git a/tests/kallisto.nf.test b/tests/kallisto.nf.test index 7720fab5e..7343798f7 100644 --- a/tests/kallisto.nf.test +++ b/tests/kallisto.nf.test @@ -49,39 +49,40 @@ nextflow_pipeline { file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( - path("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds"), - path("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds"), - path("${params.outdir}/kallisto/kallisto.merged.gene_counts.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.gene_lengths.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.gene_tpm.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds"), - path("${params.outdir}/kallisto/kallisto.merged.transcript_counts.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.transcript_lengths.tsv"), - path("${params.outdir}/kallisto/kallisto.merged.transcript_tpm.tsv"), - path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.h5"), - path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.tsv"), - path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log"), - path("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/run_info.json"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.h5"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.tsv"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/run_info.json"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.h5"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.tsv"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log"), - path("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/run_info.json"), path("${params.outdir}/kallisto/tx2gene.tsv"), - path("${params.outdir}/kallisto/WT_REP1/abundance.h5"), - path("${params.outdir}/kallisto/WT_REP1/abundance.tsv"), - path("${params.outdir}/kallisto/WT_REP1/kallisto_quant.log"), - path("${params.outdir}/kallisto/WT_REP1/run_info.json"), - path("${params.outdir}/kallisto/WT_REP2/abundance.h5"), - path("${params.outdir}/kallisto/WT_REP2/abundance.tsv"), - path("${params.outdir}/kallisto/WT_REP2/kallisto_quant.log"), - path("${params.outdir}/kallisto/WT_REP2/run_info.json") + // These files are not stable + file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.h5").name, + file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/abundance.tsv").name, + file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/kallisto_quant.log").name, + file("${params.outdir}/kallisto/RAP1_IAA_30M_REP1/run_info.json").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.h5").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/abundance.tsv").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/kallisto_quant.log").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP1/run_info.json").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.h5").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/abundance.tsv").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/kallisto_quant.log").name, + file("${params.outdir}/kallisto/RAP1_UNINDUCED_REP2/run_info.json").name, + file("${params.outdir}/kallisto/WT_REP1/abundance.h5").name, + file("${params.outdir}/kallisto/WT_REP1/abundance.tsv").name, + file("${params.outdir}/kallisto/WT_REP1/kallisto_quant.log").name, + file("${params.outdir}/kallisto/WT_REP1/run_info.json").name, + file("${params.outdir}/kallisto/WT_REP2/abundance.h5").name, + file("${params.outdir}/kallisto/WT_REP2/abundance.tsv").name, + file("${params.outdir}/kallisto/WT_REP2/kallisto_quant.log").name, + file("${params.outdir}/kallisto/WT_REP2/run_info.json").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_lengths.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.gene_tpm.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/kallisto/kallisto.merged.transcript_counts.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.transcript_lengths.tsv").name, + file("${params.outdir}/kallisto/kallisto.merged.transcript_tpm.tsv").name ).match("kallisto") }, { assert snapshot( path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), @@ -97,15 +98,15 @@ nextflow_pipeline { path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"), path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/kallisto_alignment.txt"), path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"), path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/multiqc_report_data/multiqc_kallisto.txt"), // These files are not stable file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/kallisto_alignment.txt").name, file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name, file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_kallisto.txt").name, file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name ).match("multiqc_data") }, @@ -122,12 +123,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf"), - path("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png"), - path("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg"), - path("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/multiqc_report.html").name, file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -147,11 +142,15 @@ nextflow_pipeline { file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-cnt.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/kallisto_alignment-pct.pdf").name, file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-cnt.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/kallisto_alignment-pct.png").name, file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, @@ -168,7 +167,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, - file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name + file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-cnt.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/kallisto_alignment-pct.svg").name ).match("multiqc_plots") }, { assert snapshot( // These reports are not stable diff --git a/tests/kallisto.nf.test.snap b/tests/kallisto.nf.test.snap index 5fcc98aec..2d7d3ba40 100644 --- a/tests/kallisto.nf.test.snap +++ b/tests/kallisto.nf.test.snap @@ -14,14 +14,14 @@ "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", - "kallisto_alignment.txt:md5,6f1850f735edb8c199ef69a2aeca746c", "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_kallisto.txt:md5,30343a3a84fae482f7695355726ef93a", "fastqc_top_overrepresented_sequences_table.txt", + "kallisto_alignment.txt", "multiqc_data.json", "multiqc_general_stats.txt", + "multiqc_kallisto.txt", "multiqc_software_versions.txt", "multiqc_sources.txt" ], @@ -29,7 +29,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:35:31.485152" + "timestamp": "2024-08-23T15:53:37.272547" }, "trimgalore": { "content": [ @@ -50,45 +50,45 @@ }, "kallisto": { "content": [ - "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds:md5,a3fc7ad9b88a6c706d41586ea4bebbd9", - "kallisto.merged.gene_counts_length_scaled.tsv:md5,bb825716e8d3d6b4df2d672c38e8a625", - "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds:md5,3a12e9abc26a8a5a8127425e9220e6ac", - "kallisto.merged.gene_counts_scaled.tsv:md5,ce6ece9365d45cea0a403388af8b583e", - "kallisto.merged.gene_counts.SummarizedExperiment.rds:md5,7bb079c92dd98a7c2c030212bc1affb9", - "kallisto.merged.gene_counts.tsv:md5,bf274bbe1da240633e9179851c916e02", - "kallisto.merged.gene_lengths.tsv:md5,0e55de77f556411d55c69f7e4163722b", - "kallisto.merged.gene_tpm.tsv:md5,164e18ff6f95bb56938fb08d2d40be91", - "kallisto.merged.transcript_counts.SummarizedExperiment.rds:md5,ce6ed19fb07dffa6af29598a0d845d8b", - "kallisto.merged.transcript_counts.tsv:md5,e2a2079e15d2cb31668feee3037ced48", - "kallisto.merged.transcript_lengths.tsv:md5,2c64da3760aba7789c8086d3e0e375bf", - "kallisto.merged.transcript_tpm.tsv:md5,271d646940e3b934c6e0547ea4c8fc2e", - "abundance.h5:md5,d682e51e73620ef44a7ec3285ee64273", - "abundance.tsv:md5,b6ae4ef44f718a789f58dc6451b6eebb", - "kallisto_quant.log:md5,88a4a4c71762af549f1c42308fe80605", - "run_info.json:md5,9d818e3d2ede809baf552274f15ac970", - "abundance.h5:md5,c43fb087de19af669142504061d0e3f7", - "abundance.tsv:md5,a2c6108c384662f4da8c7b7fe8f27e02", - "kallisto_quant.log:md5,b9c4528ce7c00f5f94e7570507d00a51", - "run_info.json:md5,42fc6ba7f61ea1c9fdf986859a9ebf3a", - "abundance.h5:md5,8211dd327e87d33e186373177481f0ab", - "abundance.tsv:md5,6fd77021287360f5005c90807233ab23", - "kallisto_quant.log:md5,8a9605e9d228c9cbec97b0883d909754", - "run_info.json:md5,975d7f1cc482f2a735ab064ac635ae78", "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "abundance.h5:md5,94c8aaf349b7c47bc507bf1e84d08b1b", - "abundance.tsv:md5,7b62c5df0930e9f5ebc6e90d6aa600f6", - "kallisto_quant.log:md5,5a7f563172800853c627e8e4f5da6bdc", - "run_info.json:md5,f468d320b4efcdd786ead7826e157017", - "abundance.h5:md5,a988b7e8adffd92cc9b7a096b31f83f7", - "abundance.tsv:md5,780a5d5c6d12b81f4c1865d0b9e125d3", - "kallisto_quant.log:md5,78bf71d8a5b300cc10ed119fdf69c3c0", - "run_info.json:md5,782f358803dca4a54dc7e817a4ba5776" + "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", + "run_info.json", + "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", + "run_info.json", + "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", + "run_info.json", + "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", + "run_info.json", + "abundance.h5", + "abundance.tsv", + "kallisto_quant.log", + "run_info.json", + "kallisto.merged.gene_counts.SummarizedExperiment.rds", + "kallisto.merged.gene_counts.tsv", + "kallisto.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "kallisto.merged.gene_counts_length_scaled.tsv", + "kallisto.merged.gene_counts_scaled.SummarizedExperiment.rds", + "kallisto.merged.gene_counts_scaled.tsv", + "kallisto.merged.gene_lengths.tsv", + "kallisto.merged.gene_tpm.tsv", + "kallisto.merged.transcript_counts.SummarizedExperiment.rds", + "kallisto.merged.transcript_counts.tsv", + "kallisto.merged.transcript_lengths.tsv", + "kallisto.merged.transcript_tpm.tsv" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:35:31.465634" + "timestamp": "2024-08-23T15:53:37.166056" }, "references": { "content": [ @@ -150,12 +150,6 @@ "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "kallisto_alignment-cnt.pdf:md5,1df1469743dc958991c5680bcad4d06b", - "kallisto_alignment-pct.pdf:md5,310edbb17d863cd91213e54cacc3ff28", - "kallisto_alignment-cnt.png:md5,27547934e07e17907e0f52eac50cc45c", - "kallisto_alignment-pct.png:md5,c34202594e60c3cdc1c713d066e7a381", - "kallisto_alignment-cnt.svg:md5,0112322ad8179e1a41520877a1fc0e73", - "kallisto_alignment-pct.svg:md5,5c7555a00804ef595254d12a7852d12d", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -174,11 +168,15 @@ "fastqc_sequence_length_distribution_plot.pdf", "fastqc_top_overrepresented_sequences_table.pdf", "general_stats_table.pdf", + "kallisto_alignment-cnt.pdf", + "kallisto_alignment-pct.pdf", "fastqc_per_base_n_content_plot.png", "fastqc_per_base_sequence_quality_plot.png", "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "kallisto_alignment-cnt.png", + "kallisto_alignment-pct.png", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", "cutadapt_trimmed_sequences_plot_3_Counts.svg", @@ -195,13 +193,15 @@ "fastqc_sequence_duplication_levels_plot.svg", "fastqc_sequence_length_distribution_plot.svg", "fastqc_top_overrepresented_sequences_table.svg", - "general_stats_table.svg" + "general_stats_table.svg", + "kallisto_alignment-cnt.svg", + "kallisto_alignment-pct.svg" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T15:35:31.50623" + "timestamp": "2024-08-23T15:53:37.413284" }, "bbsplit": { "content": [ From 792c80995520be0ca8c3f84ffc3eb22adbf727de Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 17:01:39 +0200 Subject: [PATCH 26/41] min_mapped_reads snapshots --- tests/min_mapped_reads.nf.test | 829 +++++++++++++++++++++++- tests/min_mapped_reads.nf.test.snap | 966 ++++++++++++++++++++++++++++ 2 files changed, 1794 insertions(+), 1 deletion(-) create mode 100644 tests/min_mapped_reads.nf.test.snap diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 9dcc7408c..394f48c0a 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -13,7 +13,834 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig") + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name + ).match("star_salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name + ).match("star_salmon/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary") + ).match("star_salmon/featurecounts") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name + ).match("star_salmon/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), + // HTML reports are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name + ).match("star_salmon/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), + // PDFs and R scripts are not stable + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name + ).match("star_salmon/rseqc") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name + ).match("star_salmon/salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name + ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, + { assert snapshot( + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name + ).match("star_salmon") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --min_mapped_reads 90") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + min_mapped_reads = 90 + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) } } } diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap new file mode 100644 index 000000000..1d6a55111 --- /dev/null +++ b/tests/min_mapped_reads.nf.test.snap @@ -0,0 +1,966 @@ +{ + "star_salmon/log": { + "content": [ + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:36:12.254374" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:36:12.719201" + }, + "star_salmon/rseqc": { + "content": [ + "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", + "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d00442929f8a18945d4597167fe3bb6d", + 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"RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:57:32.155191" + } +} \ No newline at end of file From 8c7aa24798b86b0882068f6ecfabe580e5eb37e1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 17:15:22 +0200 Subject: [PATCH 27/41] min_mapped_reads better snapshots --- tests/min_mapped_reads.nf.test | 4 ++++ tests/min_mapped_reads.nf.test.snap | 8 ++++++-- 2 files changed, 10 insertions(+), 2 deletions(-) diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 394f48c0a..615cf5bac 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -91,6 +91,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_mapped_samples_table.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), @@ -167,6 +168,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_mapped_samples_table.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), @@ -214,6 +216,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_mapped_samples_table.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, @@ -313,6 +316,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_mapped_samples_table.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 1d6a55111..018d38905 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -158,6 +158,7 @@ "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", "dupradar-section-plot.png:md5,eacbc664cc29a7a59a6aa366b4618582", + "fail_mapped_samples_table.png:md5,e0702273ab75b55895e566cb2945d893", "fastqc-status-check-heatmap-1.png:md5,2402522f8c02e12aea9af088c6595890", "fastqc-status-check-heatmap.png:md5,fe8b5b4ab4480d46a12a9005932a9b84", "fastqc_overrepresented_sequences_plot-1.png:md5,40e450251b80ec0efc9364434234ec7f", @@ -204,6 +205,7 @@ "cutadapt_trimmed_sequences_plot_3_Counts.pdf", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", "dupradar-section-plot.pdf", + "fail_mapped_samples_table.pdf", "fail_strand_check_table.pdf", "fastqc-status-check-heatmap-1.pdf", "fastqc-status-check-heatmap.pdf", @@ -303,6 +305,7 @@ "cutadapt_trimmed_sequences_plot_3_Counts.svg", "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", "dupradar-section-plot.svg", + "fail_mapped_samples_table.svg", "fail_strand_check_table.svg", "fastqc-status-check-heatmap-1.svg", "fastqc-status-check-heatmap.svg", @@ -375,7 +378,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T16:04:54.826515" + "timestamp": "2024-08-23T17:12:47.723706" }, "fastqc/raw": { "content": [ @@ -596,6 +599,7 @@ "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "multiqc_citations.txt:md5,2d2ab6df367e36e98e081c33dec187a0", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fail_mapped_samples_table.txt:md5,5dd9b06f326b1a55d78878343af89927", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", @@ -669,7 +673,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T16:04:54.775518" + "timestamp": "2024-08-23T17:12:47.537212" }, "star_salmon/deseq2_qc": { "content": [ From 33b34e7a04616fbf42776d22c7d0526772220e0f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 17:34:25 +0200 Subject: [PATCH 28/41] fix stub snap --- tests/min_mapped_reads.nf.test | 2 +- tests/min_mapped_reads.nf.test.snap | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 615cf5bac..ab2865393 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -806,7 +806,7 @@ nextflow_pipeline { } } - test("Params: --min_mapped_reads 90") { + test("Params: --min_mapped_reads 90 - stub") { options "-stub" diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 018d38905..da7d1d41f 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -936,7 +936,7 @@ }, "timestamp": "2024-08-23T16:36:12.305856" }, - "Params: --min_mapped_reads 90": { + "Params: --min_mapped_reads 90 - stub": { "content": [ "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", "genome_transcriptome.fasta", @@ -967,4 +967,4 @@ }, "timestamp": "2024-08-23T16:57:32.155191" } -} \ No newline at end of file +} From 8dd8c01217000ee2b714bd29a5e5f4837cb851ca Mon Sep 17 00:00:00 2001 From: maxulysse Date: Fri, 23 Aug 2024 18:23:00 +0200 Subject: [PATCH 29/41] remove_ribo_rna snapshots --- tests/remove_ribo_rna.nf.test | 958 +++++++++++++++++++++++- tests/remove_ribo_rna.nf.test.snap | 1102 ++++++++++++++++++++++++++++ 2 files changed, 2059 insertions(+), 1 deletion(-) create mode 100644 tests/remove_ribo_rna.nf.test.snap diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index d414d1484..c9c1a4702 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -13,7 +13,963 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/sortmerna-detailed-plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/sortmerna-detailed-plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + path("${params.outdir}/sortmerna/RAP1_IAA_30M_REP1.sortmerna.log"), + path("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP1.sortmerna.log"), + path("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP2.sortmerna.log"), + path("${params.outdir}/sortmerna/WT_REP1.sortmerna.log"), + path("${params.outdir}/sortmerna/WT_REP2.sortmerna.log") + ).match("star_salmon/sortmerna") }, + { assert snapshot( + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), + path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name + ).match("star_salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name + ).match("star_salmon/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary") + ).match("star_salmon/featurecounts") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name + ).match("star_salmon/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), + // HTML reports are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name + ).match("star_salmon/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), + path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), + // PDFs and R scripts are not stable + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + ).match("star_salmon/rseqc") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name + ).match("star_salmon/salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name + ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, + { assert snapshot( + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name + ).match("star_salmon") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --remove_ribo_rna - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + remove_ribo_rna = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) } } } diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap new file mode 100644 index 000000000..44f8ad1bc --- /dev/null +++ b/tests/remove_ribo_rna.nf.test.snap @@ -0,0 +1,1102 @@ +{ + "star_salmon/log": { + "content": [ + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T18:00:12.426991" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T18:00:13.706881" + }, + "star_salmon/rseqc": { + "content": [ + "RAP1_IAA_30M_REP1.bam_stat.txt:md5,4256d7f43715daff481bf0010b695981", + "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d04cb03c42168319cb306f0b866b6b59", + "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,5e114cb96f02f9fadd21e2a9826a68a6", + "WT_REP1.bam_stat.txt:md5,bc6521a8455de55571a3ae6ef5a07aa2", + "WT_REP2.bam_stat.txt:md5,22fd302c0f8ab19b114caa4b8d47a92c", + "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,ee69422d6e76fba223aa6b20a13027d2", + "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,ec9ec42ddfd3ffbb5373d3d6b6713b2c", + "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", + "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", + "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", + "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", + "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", + "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", + "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", + "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", + "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", + "WT_REP1.junction.Interact.bed:md5,2132b64829f397caeb41b3b4eaa8eadf", + "WT_REP1.junction.bed:md5,f9214aec5c178ffae736308615d2535e", + "WT_REP2.junction.Interact.bed:md5,0da2295d05c6a5de213c2172350ba87e", + "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", + "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", + "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", + "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", + "WT_REP1.junction_annotation.log:md5,e26d4111fd4e731a9f2a10fcadee9090", + "WT_REP2.junction_annotation.log:md5,1b95af725477bbe771ed4e7b7d693729", + "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", + "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", + "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", + "WT_REP1.junction_plot.r:md5,3a6e7f258151c69d3472d7ac3afe19f1", + "WT_REP2.junction_plot.r:md5,146b3da40cd5944c3eabc6e948fd8e44", + "RAP1_IAA_30M_REP1.junction.xls:md5,ce9d38109ceabb83e1349cc1a8779e3f", + "RAP1_UNINDUCED_REP1.junction.xls:md5,34204ec2f7648de90070ec9687c05cb2", + "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", + "WT_REP1.junction.xls:md5,d25b37752ce12695ef08c2842a0c01b1", + "WT_REP2.junction.xls:md5,1a3c7d9a4ac9159b87caa1f4ef4b6748", + "RAP1_IAA_30M_REP1.read_distribution.txt:md5,37fadf8a5d3e6d4276fdcc217a0df8ab", + "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,ac45c5dfa40382fd2613c85754dde373", + "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,de16f30d41f987f875e880bd3356d3f0", + "WT_REP1.read_distribution.txt:md5,b72fac25d0cf554a657029290ca20bdd", + "WT_REP2.read_distribution.txt:md5,9042fc9da71efb3f68ab254088dcba54", + "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,afe0a648fafb80250e6d67865bbbfc3f", + "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,e900364ed504bfb704295345471e39ed", + "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,6b3800c7ee5d1b873fa9c1f5ddfa3449", + "WT_REP1.DupRate_plot.r:md5,99bcfa0636316c8681a80b284a733867", + "WT_REP2.DupRate_plot.r:md5,9e531ac620795015672007456755a90f", + "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,825f80662e5525c3303fc63b741e908c", + "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,e54f45dcc2e2cdebcd86602dbf938538", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,73c39a8c11fa0b1c94025942ca9d5d41", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,80e5b2b1ce48edc1c6a7deeff69f5fce", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,d3aa129590e9fec24c01c39f09f7e734", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,5f017f8cd9b254daeeae0b5e7b74bed7", + "WT_REP1.pos.DupRate.xls:md5,f1ce288eec6e9ad760c6499cfe9e6ff9", + "WT_REP1.seq.DupRate.xls:md5,7e1b37c441fa9d05d584931ec5d7042f", + "WT_REP2.pos.DupRate.xls:md5,bba919e65f7001299bda2980da0e08a9", + "WT_REP2.seq.DupRate.xls:md5,9b15bcb5b3634f8dfe177e859ee40582", + "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", + "WT_REP1.inner_distance_plot.pdf", + "WT_REP2.inner_distance_plot.pdf", + "RAP1_IAA_30M_REP1.inner_distance_plot.r", + "WT_REP1.inner_distance_plot.r", + "WT_REP2.inner_distance_plot.r", + "RAP1_IAA_30M_REP1.inner_distance.txt", + "RAP1_IAA_30M_REP1.inner_distance_freq.txt", + "RAP1_IAA_30M_REP1.inner_distance_mean.txt", + "WT_REP1.inner_distance.txt", + "WT_REP1.inner_distance_freq.txt", + "WT_REP1.inner_distance_mean.txt", + "WT_REP2.inner_distance.txt", + "WT_REP2.inner_distance_freq.txt", + "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.splice_events.pdf", + "RAP1_IAA_30M_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP1.splice_events.pdf", + "RAP1_UNINDUCED_REP1.splice_junction.pdf", + "RAP1_UNINDUCED_REP2.splice_events.pdf", + "RAP1_UNINDUCED_REP2.splice_junction.pdf", + "WT_REP1.splice_events.pdf", + "WT_REP1.splice_junction.pdf", + 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Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 09:50:25 +0200 Subject: [PATCH 30/41] update remove_ribo_rna snapshots --- tests/remove_ribo_rna.nf.test | 11 ++++++----- tests/remove_ribo_rna.nf.test.snap | 12 ++++++------ 2 files changed, 12 insertions(+), 11 deletions(-) diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index c9c1a4702..2df0dace9 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -483,11 +483,12 @@ nextflow_pipeline { file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name ).match("salmon") }, { assert snapshot( - path("${params.outdir}/sortmerna/RAP1_IAA_30M_REP1.sortmerna.log"), - path("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP1.sortmerna.log"), - path("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP2.sortmerna.log"), - path("${params.outdir}/sortmerna/WT_REP1.sortmerna.log"), - path("${params.outdir}/sortmerna/WT_REP2.sortmerna.log") + // These files are not stable + file("${params.outdir}/sortmerna/RAP1_IAA_30M_REP1.sortmerna.log").name, + file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP1.sortmerna.log").name, + file("${params.outdir}/sortmerna/RAP1_UNINDUCED_REP2.sortmerna.log").name, + file("${params.outdir}/sortmerna/WT_REP1.sortmerna.log").name, + file("${params.outdir}/sortmerna/WT_REP2.sortmerna.log").name ).match("star_salmon/sortmerna") }, { assert snapshot( path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 44f8ad1bc..dc0aa231a 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -940,11 +940,11 @@ }, "star_salmon/sortmerna": { "content": [ - "RAP1_IAA_30M_REP1.sortmerna.log:md5,2fe1896779708960052299a1b3bc22e2", - "RAP1_UNINDUCED_REP1.sortmerna.log:md5,8866cd5eb622ea19a793fc63f232ea05", - "RAP1_UNINDUCED_REP2.sortmerna.log:md5,d905e5b8b51ad7c9524aa7aee8c55dc2", - "WT_REP1.sortmerna.log:md5,bf37a10e24b436cdef0d20eef5fedecc", - "WT_REP2.sortmerna.log:md5,e7decfb65071a73c0b7a3c43f3530077" + "RAP1_IAA_30M_REP1.sortmerna.log", + "RAP1_UNINDUCED_REP1.sortmerna.log", + "RAP1_UNINDUCED_REP2.sortmerna.log", + "WT_REP1.sortmerna.log", + "WT_REP2.sortmerna.log" ], "meta": { "nf-test": "0.9.0", @@ -1099,4 +1099,4 @@ }, "timestamp": "2024-08-23T18:00:12.786569" } -} \ No newline at end of file +} From 51b1b0fb92599313bd96f285628ccb25cd43589c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 10:40:52 +0200 Subject: [PATCH 31/41] salmon snapshots + update moar snapshots --- tests/hisat2.nf.test | 3 +- tests/remove_ribo_rna.nf.test | 4 +- tests/remove_ribo_rna.nf.test.snap | 8 +- tests/salmon.nf.test | 253 +++++++++++++++++++++++- tests/salmon.nf.test.snap | 297 +++++++++++++++++++++++++++++ 5 files changed, 557 insertions(+), 8 deletions(-) create mode 100644 tests/salmon.nf.test.snap diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index f9560c7ba..8ee660e05 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -797,7 +797,8 @@ nextflow_pipeline { file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name - ).match("salmon") }, { assert snapshot( + ).match("salmon") }, + { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 2df0dace9..1242c1fbe 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -99,7 +99,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), @@ -119,7 +118,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -140,6 +138,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sortmerna.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, @@ -160,6 +159,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index dc0aa231a..0d0ef618a 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -705,7 +705,6 @@ "multiqc_rseqc_junction_annotation.txt:md5,e67493668e9b93f6e15c145d8d844372", "multiqc_rseqc_read_distribution.txt:md5,0132183561c399a5b57eee5f82bda19e", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "multiqc_sortmerna.txt:md5,1171fc564e1bfadb49d892535c38c8b6", "picard_deduplication.txt:md5,32d912bd78e7d99276a52e13575d08aa", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -725,7 +724,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", "samtools_alignment_plot.txt:md5,207e0c3f557679f37350577364b8956d", - "sortmerna-detailed-plot.txt:md5,b93dadb4ca77c6af68ef2c00a8626f17", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -745,6 +743,7 @@ "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", + "multiqc_sortmerna.txt", "multiqc_sources.txt", "multiqc_star.txt", "multiqc_star_salmon_deseq2_clustering-plot.txt", @@ -765,6 +764,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "sortmerna-detailed-plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -772,7 +772,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:18:51.71382" + "timestamp": "2024-08-26T10:39:39.81199" }, "star_salmon/deseq2_qc": { "content": [ @@ -1099,4 +1099,4 @@ }, "timestamp": "2024-08-23T18:00:12.786569" } -} +} \ No newline at end of file diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index cf0a2d93e..491bdc999 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -15,7 +15,258 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + // These files are not stable + file("${params.outdir}/multiqc/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/multiqc_report_data/salmon_plot.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/multiqc_report.html").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/multiqc_report_plots/svg/salmon_plot.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) } } } diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap new file mode 100644 index 000000000..356d970b3 --- /dev/null +++ b/tests/salmon.nf.test.snap @@ -0,0 +1,297 @@ +{ + "multiqc_data": { + "content": [ + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_sequence_counts_plot.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "multiqc_citations.txt:md5,f789abe663d4b4214f0ddeb413a7f150", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "fastqc_top_overrepresented_sequences_table.txt", + "multiqc_data.json", + "multiqc_general_stats.txt", + "multiqc_salmon.txt", + "multiqc_software_versions.txt", + "multiqc_sources.txt", + "salmon_plot.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.703525" + }, + "trimgalore": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.861436" + }, + "references": { + "content": [ + "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", + "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.678308" + }, + "versions": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, SALMON_QUANT={salmon=1.10.1}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:10.110511" + }, + "fastqc/trim": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.69038" + }, + "salmon": { + "content": [ + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "salmon.merged.gene_counts.SummarizedExperiment.rds", + "salmon.merged.gene_counts.tsv", + "salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds", + "salmon.merged.gene_counts_length_scaled.tsv", + "salmon.merged.gene_counts_scaled.SummarizedExperiment.rds", + "salmon.merged.gene_counts_scaled.tsv", + "salmon.merged.gene_lengths.tsv", + "salmon.merged.gene_tpm.tsv", + "salmon.merged.transcript_counts.SummarizedExperiment.rds", + "salmon.merged.transcript_counts.tsv", + "salmon.merged.transcript_lengths.tsv", + "salmon.merged.transcript_tpm.tsv" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.804203" + }, + "multiqc_plots": { + "content": [ + "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", + "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", + "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.png:md5,1e0d01537d3797623d0b3fd8fbe42787", + "fastqc-status-check-heatmap.png:md5,2402522f8c02e12aea9af088c6595890", + "fastqc_overrepresented_sequences_plot.png:md5,40e450251b80ec0efc9364434234ec7f", + "fastqc_per_sequence_gc_content_plot_Counts.png:md5,8a806cec2142f9911502e0a253d83d13", + "fastqc_per_sequence_gc_content_plot_Percentages.png:md5,953929d50c8490029880e205e4db7959", + "fastqc_per_sequence_quality_scores_plot.png:md5,d2c29cae169f35744500c751b4a7366e", + "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", + "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", + "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", + "multiqc_report.html", + "cutadapt_filtered_reads_plot-cnt.pdf", + "cutadapt_filtered_reads_plot-pct.pdf", + "cutadapt_trimmed_sequences_plot_3_Counts.pdf", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", + "fastqc-status-check-heatmap.pdf", + "fastqc_overrepresented_sequences_plot.pdf", + "fastqc_per_base_n_content_plot.pdf", + "fastqc_per_base_sequence_quality_plot.pdf", + "fastqc_per_sequence_gc_content_plot_Counts.pdf", + "fastqc_per_sequence_gc_content_plot_Percentages.pdf", + "fastqc_per_sequence_quality_scores_plot.pdf", + "fastqc_sequence_counts_plot-cnt.pdf", + "fastqc_sequence_counts_plot-pct.pdf", + "fastqc_sequence_duplication_levels_plot.pdf", + "fastqc_sequence_length_distribution_plot.pdf", + "fastqc_top_overrepresented_sequences_table.pdf", + "general_stats_table.pdf", + "salmon_plot.pdf", + "fastqc_per_base_n_content_plot.png", + "fastqc_per_base_sequence_quality_plot.png", + "fastqc_sequence_length_distribution_plot.png", + "fastqc_top_overrepresented_sequences_table.png", + "general_stats_table.png", + "salmon_plot.png", + "cutadapt_filtered_reads_plot-cnt.svg", + "cutadapt_filtered_reads_plot-pct.svg", + "cutadapt_trimmed_sequences_plot_3_Counts.svg", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", + "fastqc-status-check-heatmap.svg", + "fastqc_overrepresented_sequences_plot.svg", + "fastqc_per_base_n_content_plot.svg", + "fastqc_per_base_sequence_quality_plot.svg", + "fastqc_per_sequence_gc_content_plot_Counts.svg", + "fastqc_per_sequence_gc_content_plot_Percentages.svg", + "fastqc_per_sequence_quality_scores_plot.svg", + "fastqc_sequence_counts_plot-cnt.svg", + "fastqc_sequence_counts_plot-pct.svg", + "fastqc_sequence_duplication_levels_plot.svg", + "fastqc_sequence_length_distribution_plot.svg", + "fastqc_top_overrepresented_sequences_table.svg", + "general_stats_table.svg", + "salmon_plot.svg" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.724424" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.665867" + }, + "salmon_quant": { + "content": [ + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:09.758031" + }, + "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", + "genome_transcriptome.fasta", + "genome_transcriptome.gtf", + "RAP1_IAA_30M_REP1_raw.html", + "RAP1_IAA_30M_REP1_raw.zip", + "RAP1_UNINDUCED_REP1_raw.html", + "RAP1_UNINDUCED_REP1_raw.zip", + "RAP1_UNINDUCED_REP2_raw.html", + "RAP1_UNINDUCED_REP2_raw.zip", + "WT_REP1_raw.html", + "WT_REP1_raw.zip", + "WT_REP2_raw.html", + "WT_REP2_raw.zip", + "multiqc_report.html", + "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", + "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", + "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T10:25:58.654392" + } +} \ No newline at end of file From 14266165e9d582f5a0710de6d35076e9962843fb Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 12:37:11 +0200 Subject: [PATCH 32/41] skip_qc snapshots --- tests/salmon.nf.test | 3 + tests/skip_qc.nf.test | 510 ++++++++++++++++++++++++++++++- tests/skip_qc.nf.test.snap | 596 +++++++++++++++++++++++++++++++++++++ 3 files changed, 1108 insertions(+), 1 deletion(-) create mode 100644 tests/skip_qc.nf.test.snap diff --git a/tests/salmon.nf.test b/tests/salmon.nf.test index 491bdc999..9105ed9fa 100644 --- a/tests/salmon.nf.test +++ b/tests/salmon.nf.test @@ -236,6 +236,9 @@ nextflow_pipeline { when { params { outdir = "$outputDir" + pseudo_aligner = 'salmon' + skip_qc = true + skip_alignment = true } } diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index db718462e..410aa5a1b 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -13,7 +13,515 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name + ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name + ).match("star_salmon/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name + ).match("star_salmon/salmon_quant") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name + ).match("star_salmon/salmon") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --skip_qc - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + skip_qc = true + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) } } } diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap new file mode 100644 index 000000000..514f7b216 --- /dev/null +++ b/tests/skip_qc.nf.test.snap @@ -0,0 +1,596 @@ +{ + "star_salmon/log": { + "content": [ + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,ea95e243278af55534f2c52eb5fff7ee", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,e548d13942535dc0821f3ec6d9743ec8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1f294365343a1a5e95682792fdb77033", + "WT_REP1.SJ.out.tab:md5,1350c2fa6a675bf107386c6cd3fc5204", + "WT_REP2.SJ.out.tab:md5,f6cc03643a5e3c1025a5b4754eb1be23", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:11:58.323422" + }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + 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"meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:11:57.943545" + }, + "versions": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, BEDTOOLS_GENOMECOV_FW={bedtools=2.31.1}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=3.9.5}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, CUSTOM_TX2GENE={python=3.9.5}, FQ_SUBSAMPLE={fq=0.9.1 (2022-02-22)}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, PICARD_MARKDUPLICATES={picard=3.1.1}, SALMON_QUANT={salmon=1.10.1}, SAMTOOLS_FLAGSTAT={samtools=1.2}, SAMTOOLS_IDXSTATS={samtools=1.2}, SAMTOOLS_INDEX={samtools=1.2}, SAMTOOLS_SORT={samtools=1.2}, SAMTOOLS_STATS={samtools=1.2}, SE_GENE={bioconductor-summarizedexperiment=1.32.0}, STAR_ALIGN={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, STRINGTIE_STRINGTIE={stringtie=2.2.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, TXIMETA_TXIMPORT={bioconductor-tximeta=1.20.1}, UCSC_BEDCLIP={ucsc=377}, UCSC_BEDGRAPHTOBIGWIG={ucsc=445}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:11:59.164489" + }, + "fastqc/trim": { + "content": [ + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html", + "RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html", + "RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip", + "WT_REP1_trimmed_1_val_1_fastqc.html", + "WT_REP1_trimmed_1_val_1_fastqc.zip", + "WT_REP1_trimmed_2_val_2_fastqc.html", + "WT_REP1_trimmed_2_val_2_fastqc.zip", + "WT_REP2_trimmed_1_val_1_fastqc.html", + "WT_REP2_trimmed_1_val_1_fastqc.zip", + "WT_REP2_trimmed_2_val_2_fastqc.html", + "WT_REP2_trimmed_2_val_2_fastqc.zip" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:24:48.114664" + }, + "bbsplit": { + "content": [ + "RAP1_IAA_30M_REP1.stats.txt", + "RAP1_UNINDUCED_REP1.stats.txt", + "RAP1_UNINDUCED_REP2.stats.txt", + "WT_REP1.stats.txt", + "WT_REP2.stats.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T11:24:48.0918" + }, + "salmon_quant": { + "content": [ + "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,1215f0c20f87d3aef8553ef119e1e74c", + "lib_format_counts.json:md5,c24ffe28d70476b5ccdd8bc2d22c0ac1", + "ambig_info.tsv:md5,45f252b4f0e11e6730cf0c29f800fdbb", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,621c6601aade5b1f2e3d6ca2fc71f636", + "lib_format_counts.json:md5,f6d44c0221f7fd559f11a9afe04c9935", + "ambig_info.tsv:md5,6dcc2891ea572e9b8d1ba52cd434ab84", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,9bed6e4dc5428d6f6297adcea29a6326", + "lib_format_counts.json:md5,7c562bf2f70e42f3a7292687dfd328c3", + "ambig_info.tsv:md5,194f574e0586416155e3f33d42e2b167", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,c7ed0aaa5d6c7934ddbebfd29e4eb86d", + "lib_format_counts.json:md5,d46250bb3677d72feeefc435fe6395a6", + "ambig_info.tsv:md5,a26e3f936e65d7da66392603c2f91f6f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,69ebfc2c7ca6b221a0a22fa1dc8c20ac", + "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T12:11:58.071145" + } +} \ No newline at end of file From 3cf398a86514fae2e0c6dabd19d0684e4f141486 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 13:22:59 +0200 Subject: [PATCH 33/41] update tests and snapshots --- tests/default.nf.test | 223 ++++++------ tests/default.nf.test.snap | 356 ++++++++++---------- tests/featurecounts_group_type.nf.test | 212 ++++++------ tests/featurecounts_group_type.nf.test.snap | 170 +++++----- tests/hisat2.nf.test | 220 ++++++------ tests/hisat2.nf.test.snap | 32 +- tests/min_mapped_reads.nf.test | 154 ++++----- tests/min_mapped_reads.nf.test.snap | 352 +++++++++---------- tests/remove_ribo_rna.nf.test | 222 ++++++------ tests/remove_ribo_rna.nf.test.snap | 356 ++++++++++---------- tests/salmon.nf.test.snap | 2 +- 11 files changed, 1155 insertions(+), 1144 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index a74bdf491..ca3929641 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -94,9 +94,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), @@ -104,15 +101,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -126,7 +117,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, @@ -145,14 +139,20 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, @@ -188,15 +188,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -290,12 +284,18 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, @@ -474,16 +474,17 @@ nextflow_pipeline { file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name ).match("salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), @@ -531,23 +532,24 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary") + // These files are unstable + file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name ).match("star_salmon/featurecounts") }, { assert snapshot( path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), @@ -584,117 +586,72 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), - // HTML reports are not stable + // HTML reports and these files are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name + file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name ).match("star_salmon/qualimap") }, { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), - // PDFs and R scripts are not stable + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, @@ -710,6 +667,21 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, @@ -720,6 +692,16 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, @@ -730,11 +712,31 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("star_salmon/rseqc") }, { assert snapshot( // These files are not stable @@ -754,34 +756,35 @@ nextflow_pipeline { { assert snapshot( path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), @@ -896,7 +899,7 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon") }, + ).match("star_salmon/salmon_quant") }, { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 387cc6451..330a0bc6e 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -28,6 +28,71 @@ }, "timestamp": "2024-08-22T14:57:58.85709" }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:24:55.413942" + }, "trimgalore": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", @@ -47,61 +112,16 @@ }, "star_salmon/rseqc": { "content": [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d00442929f8a18945d4597167fe3bb6d", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,447c12933610cb3e0aeb4560906332c6", - "WT_REP1.bam_stat.txt:md5,85d14e5c3943407e636186424fd766cb", - "WT_REP2.bam_stat.txt:md5,12ae5d98f3e5cf7b3a70eed45f12cbe2", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", - "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", - "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", - "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", - "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", - "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", - "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", - "WT_REP1.junction.Interact.bed:md5,a989d63b778be8daa2df6ea57ac3fc93", - "WT_REP1.junction.bed:md5,a0082fba0e4222d41fc5e5c6ba6db453", - "WT_REP2.junction.Interact.bed:md5,0da2295d05c6a5de213c2172350ba87e", - "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", - "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", - "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", - "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", - "WT_REP1.junction_annotation.log:md5,93ff20da87153de88c5686588330abd2", - "WT_REP2.junction_annotation.log:md5,1b95af725477bbe771ed4e7b7d693729", - "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", - "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", - "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", - "WT_REP1.junction_plot.r:md5,1ffa6c2df67179c4335fb79db597ad50", - "WT_REP2.junction_plot.r:md5,146b3da40cd5944c3eabc6e948fd8e44", - "RAP1_IAA_30M_REP1.junction.xls:md5,ce9d38109ceabb83e1349cc1a8779e3f", - "RAP1_UNINDUCED_REP1.junction.xls:md5,34204ec2f7648de90070ec9687c05cb2", - "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", - "WT_REP1.junction.xls:md5,02119fa98515474e525ea86ddd1b189c", - "WT_REP2.junction.xls:md5,1a3c7d9a4ac9159b87caa1f4ef4b6748", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,a181a8045a4aaee911e6acd60cc25d43", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,1d91e11972e9b0a55035f4d9b2fa9b86", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,ece206e073f3410f6e40d2ff91c9a714", - "WT_REP1.read_distribution.txt:md5,7521690f215bf27fe161b8e6d7c38769", - "WT_REP2.read_distribution.txt:md5,c11d02cba5674017b90c8372abee3e39", - "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,0505b253ebe3a21cb06a04a08c9313dd", - "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,630db79b02077966911b521a1894e1e1", - "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,4c7cbbb403a09b1056591772867977bd", - "WT_REP1.DupRate_plot.r:md5,99e3eac32a2a2b508501c35c1cccd2bc", - "WT_REP2.DupRate_plot.r:md5,c61f96c3761940feed3f60950ef8ac84", - "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,28c98318b0858f06987d3769228dfffb", - "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,8ab97ebe54912525b971bf82f2ff08a6", - "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,01d81e64075b8381f8467cf7b7601ea1", - "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,070f3b1f484e2603fb61ac34bfb531c4", - "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,3ba876c7a04c1c81260f823f0060c7ac", - "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,941ee93c523c226aad6e6304e9c427e7", - "WT_REP1.pos.DupRate.xls:md5,aba7ea30dc35e376f7655ef298fcaf1c", - "WT_REP1.seq.DupRate.xls:md5,44355ee29233ddd150cd9542e807cc1a", - "WT_REP2.pos.DupRate.xls:md5,c683b1637e778113bb0a75843ff290af", - "WT_REP2.seq.DupRate.xls:md5,ab100995d906dcd338ec8f7f8a6d3fe0", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP2.bam_stat.txt", + "WT_REP1.bam_stat.txt", + "WT_REP2.bam_stat.txt", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", "WT_REP1.inner_distance_plot.pdf", "WT_REP2.inner_distance_plot.pdf", @@ -117,6 +137,21 @@ "WT_REP2.inner_distance.txt", "WT_REP2.inner_distance_freq.txt", "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_UNINDUCED_REP1.junction.Interact.bed", + "RAP1_UNINDUCED_REP1.junction.bed", + "RAP1_UNINDUCED_REP2.junction.Interact.bed", + "RAP1_UNINDUCED_REP2.junction.bed", + "WT_REP1.junction.Interact.bed", + "WT_REP1.junction.bed", + "WT_REP2.junction.Interact.bed", + "WT_REP2.junction.bed", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP2.junction_annotation.log", + "WT_REP1.junction_annotation.log", + "WT_REP2.junction_annotation.log", "RAP1_IAA_30M_REP1.splice_events.pdf", "RAP1_IAA_30M_REP1.splice_junction.pdf", "RAP1_UNINDUCED_REP1.splice_events.pdf", @@ -127,6 +162,16 @@ "WT_REP1.splice_junction.pdf", "WT_REP2.splice_events.pdf", "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP2.junction_plot.r", + "WT_REP1.junction_plot.r", + "WT_REP2.junction_plot.r", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_UNINDUCED_REP1.junction.xls", + "RAP1_UNINDUCED_REP2.junction.xls", + "WT_REP1.junction.xls", + "WT_REP2.junction.xls", "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", @@ -137,17 +182,37 @@ "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", "WT_REP1.junctionSaturation_plot.r", "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP2.read_distribution.txt", + "WT_REP1.read_distribution.txt", + "WT_REP2.read_distribution.txt", "RAP1_IAA_30M_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", "WT_REP1.DupRate_plot.pdf", - "WT_REP2.DupRate_plot.pdf" + "WT_REP2.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP2.DupRate_plot.r", + "WT_REP1.DupRate_plot.r", + "WT_REP2.DupRate_plot.r", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "WT_REP1.pos.DupRate.xls", + "WT_REP1.seq.DupRate.xls", + "WT_REP2.pos.DupRate.xls", + "WT_REP2.seq.DupRate.xls" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T15:35:07.931345" + "timestamp": "2024-08-26T12:44:57.857714" }, "references": { "content": [ @@ -164,40 +229,40 @@ "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats:md5,343fed237246c2fa05448ee35f6ca576", "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.stats:md5,e32e72af9ed78cc2bd7b13f9a346b1ae", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats:md5,670e8e469a04f4f23c6a9e9f618a9fff", "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.stats:md5,0abe3a520e6c91ed95f58f0f0a78315e", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats:md5,2b6cb09b61cf70580facfd19f7830fbc", "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.stats:md5,1f52bfe3684e46e19c6f03d446cfb997", "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.markdup.sorted.bam.stats:md5,cace1fe9ae48456da96b12892a545b75", "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.stats:md5,52589c03e46d86f8d39edd7c05acf11c", "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.markdup.sorted.bam.stats:md5,c2b2c16839be7d46cc38bfce6f3aeac4", "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.stats:md5,5df70efbdf409f561d86074859e4dfa9" + "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:56.229676" + "timestamp": "2024-08-26T12:44:57.974787" }, "Params: default - stub": { "content": [ @@ -259,15 +324,9 @@ "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", - "qualimap_genomic_origin-cnt.png:md5,49c63998f83c3220a35cd4839bf7fecd", - "qualimap_genomic_origin-pct.png:md5,ab6697c27cf430782bda984483e708e9", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,1003e4b5012bbddc40badd9e2dfdda8e", - "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,676644afc0aee6f63c1299b691b2b93f", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,e7636c4fcd19e7b7bb1731ac7e60d7ea", - "rseqc_read_distribution_plot-cnt.png:md5,7940585c2e998d91a608ac48716c4ab1", - "rseqc_read_distribution_plot-pct.png:md5,b6a312b41ed143a7cd8f19a3dd23696d", "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -360,12 +419,18 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "qualimap_genomic_origin-cnt.png", + "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png", + "rseqc_junction_annotation_junctions_plot_Events-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", @@ -454,7 +519,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T16:18:50.128016" + "timestamp": "2024-08-26T12:44:57.525336" }, "fastqc/raw": { "content": [ @@ -530,71 +595,6 @@ }, "timestamp": "2024-08-22T15:35:08.116582" }, - "star_salmon": { - "content": [ - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T13:24:55.413942" - }, "salmon_quant": { "content": [ "ambig_info.tsv:md5,de973a4b22a4457217ae3dc04caf9401", @@ -695,9 +695,6 @@ "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", - "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", - "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", - "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -705,15 +702,9 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", - "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", - "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", - "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -726,7 +717,10 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", + "multiqc_rseqc_junction_annotation.txt", + "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -745,14 +739,20 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "qualimap_genomic_origin.txt", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", @@ -764,7 +764,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T16:18:49.968848" + "timestamp": "2024-08-26T12:44:57.429315" }, "star_salmon/deseq2_qc": { "content": [ @@ -810,29 +810,29 @@ "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", - "RAP1_IAA_30M_REP1.featureCounts.txt.summary:md5,350e320b341a252ecfb569d4f412a02e", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", - "RAP1_UNINDUCED_REP1.featureCounts.txt.summary:md5,2b834f8b69c28d80ccfc51440bc693ff", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", - "RAP1_UNINDUCED_REP2.featureCounts.txt.summary:md5,1c69f066c7457c2633f4f90f322744fc", "WT_REP1.biotype_counts_mqc.tsv:md5,cac41767a8cc2e5fee58637971ec89d1", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,112001ddbe917d935ee276d1685840bd", - "WT_REP1.featureCounts.txt.summary:md5,63cbb69debf598f7d31848f5044ccc98", "WT_REP2.biotype_counts_mqc.tsv:md5,e61b72317ac3c4d4ac64b663145e6262", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,59e23ae18cfe6aa2e5a884bc03cbff15", - "WT_REP2.featureCounts.txt.summary:md5,1c83b365175ed49c0c70903c7daffef6" + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.featureCounts.txt.summary", + "WT_REP2.featureCounts.txt.summary" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:55.089501" + "timestamp": "2024-08-26T12:44:57.630756" }, "salmon/deseq2_qc": { "content": [ @@ -913,16 +913,16 @@ }, "star_salmon/bigwig": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466", - "WT_REP1.forward.bigWig:md5,92ad01ddd1dbb7f6d7e2eae23df58c7c", - "WT_REP1.reverse.bigWig:md5,dcac37ef5fff108afd0632388919dcf7", - "WT_REP2.forward.bigWig:md5,d10cbea27b82745b46077191d3ff2820", - "WT_REP2.reverse.bigWig:md5,2b3a15b511efdbc838574200ee2bec0c" + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig", + "WT_REP1.forward.bigWig", + "WT_REP1.reverse.bigWig", + "WT_REP2.forward.bigWig", + "WT_REP2.reverse.bigWig" ], "meta": { "nf-test": "0.9.0", @@ -1018,63 +1018,63 @@ "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", - "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", - "Reads Genomic Origin.png:md5,477fbfe923c7d416b507fb488f659ba9", "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", - "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", - "Reads Genomic Origin.png:md5,e19e85335cf6f64495f4691f15cf39d8", "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", - "Junction Analysis.png:md5,39ac823182971b41faec683b981cfcfa", - "Reads Genomic Origin.png:md5,1c0624213e8627aa2496d045117a4fe8", "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", "Coverage Profile Along Genes (High).png:md5,c974d47996bcc57b99dfaf6903f61f41", "Coverage Profile Along Genes (Low).png:md5,c8fe631f0580c93adb5be107c6a7a1a3", "Coverage Profile Along Genes (Total).png:md5,424d245e9f3e626d9e79f51d1b93e946", - "Junction Analysis.png:md5,91f986214d4367ca124d0c1e79ebdf61", - "Reads Genomic Origin.png:md5,c99bbcf2882d7ab7a0093157faa69c72", "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6", "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5", "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b", - "Junction Analysis.png:md5,147d7341869d7446ae0ad4dd1e3de700", - "Reads Genomic Origin.png:md5,93e1f3e32fa60a4dddc4ca696e1347f0", "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", - "qualimapReport.html" + "rnaseq_qc_results.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T13:59:55.673329" + "timestamp": "2024-08-26T12:44:57.740534" } } \ No newline at end of file diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index b70c359ee..4d79c7ae8 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -94,9 +94,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), @@ -104,15 +101,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -126,7 +117,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, @@ -145,14 +139,20 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, @@ -186,15 +186,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -286,12 +280,18 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctio.namens_plot_Events-cnt.png"), + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, @@ -468,16 +468,17 @@ nextflow_pipeline { file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name ).match("salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), @@ -556,117 +557,72 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), - // HTML reports are not stable + // HTML reports and these files are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name + file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name ).match("star_salmon/qualimap") }, { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), - // PDFs and R scripts are not stable + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, @@ -682,6 +638,21 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, @@ -692,6 +663,16 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, @@ -702,11 +683,31 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("star_salmon/rseqc") }, { assert snapshot( // These files are not stable @@ -726,34 +727,35 @@ nextflow_pipeline { { assert snapshot( path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), @@ -868,7 +870,7 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon") }, + ).match("star_salmon/salmon_quant") }, { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 632aa0d17..3c11ea4c9 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -28,6 +28,71 @@ }, "timestamp": "2024-08-22T17:43:26.652121" }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T13:34:18.439694" + }, "multiqc_data": { "content": [ "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", @@ -58,9 +123,6 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", - "multiqc_rseqc_bam_stat.txt:md5,1aa9eeb5b9d283ba77e98f0f5ea0f712", - "multiqc_rseqc_junction_annotation.txt:md5,e78e23f7f32cc2c58136df6ed89d7638", - "multiqc_rseqc_read_distribution.txt:md5,b7106d48346fe4150a8094ef1744f8b3", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -68,15 +130,9 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,02044ed1bf1eca19a8a87c9971cdc049", "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", - "qualimap_genomic_origin.txt:md5,bf9f1cba02195a298fb54c984c3269a6", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", - "qualimap_rnaseq_genome_results.txt:md5,ce5f4f7f5afa8f1e5666f738c4f414e7", - "rseqc_bam_stat.txt:md5,ba2575875efaf137f8bf7c2b790d5b1b", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,90f1fabea84aa36f647b980978d01e58", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", - "rseqc_read_distribution_plot.txt:md5,48cea394a38d0f0ed3044b0a54638e65", - "rseqc_read_dups_plot.txt:md5,a9f437a3a7eaeb2709fa63644de16ea0", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -89,7 +145,10 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", + "multiqc_rseqc_junction_annotation.txt", + "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -108,14 +167,20 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "qualimap_genomic_origin.txt", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", @@ -127,7 +192,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:34:58.105874" + "timestamp": "2024-08-26T12:52:52.937207" }, "trimgalore": { "content": [ @@ -663,16 +728,16 @@ }, "star_salmon/bigwig": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466", - "WT_REP1.forward.bigWig:md5,92ad01ddd1dbb7f6d7e2eae23df58c7c", - "WT_REP1.reverse.bigWig:md5,dcac37ef5fff108afd0632388919dcf7", - "WT_REP2.forward.bigWig:md5,d10cbea27b82745b46077191d3ff2820", - "WT_REP2.reverse.bigWig:md5,2b3a15b511efdbc838574200ee2bec0c" + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig", + "WT_REP1.forward.bigWig", + "WT_REP1.reverse.bigWig", + "WT_REP2.forward.bigWig", + "WT_REP2.reverse.bigWig" ], "meta": { "nf-test": "0.9.0", @@ -770,71 +835,6 @@ }, "timestamp": "2024-08-22T17:43:26.873868" }, - "star_salmon": { - "content": [ - "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", - "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T13:34:18.439694" - }, "fastqc/trim": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html", diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 8ee660e05..46c65ae09 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -66,16 +66,17 @@ nextflow_pipeline { file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name ).match("fastqc/trim") }, { assert snapshot( - path("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), - path("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), - path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), - path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), - path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), - path("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), - path("${params.outdir}/hisat2/bigwig/WT_REP1.forward.bigWig"), - path("${params.outdir}/hisat2/bigwig/WT_REP1.reverse.bigWig"), - path("${params.outdir}/hisat2/bigwig/WT_REP2.forward.bigWig"), - path("${params.outdir}/hisat2/bigwig/WT_REP2.reverse.bigWig") + // These files are not stable + file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/hisat2/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/hisat2/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/hisat2/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/hisat2/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/hisat2/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/hisat2/bigwig/WT_REP2.reverse.bigWig").name ).match("hisat2/bigwig") }, { assert snapshot( path("${params.outdir}/hisat2/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), @@ -109,23 +110,23 @@ nextflow_pipeline { path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt.summary"), path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt"), - path("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary") + file("${params.outdir}/hisat2/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/hisat2/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, + file("${params.outdir}/hisat2/featurecounts/WT_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/hisat2/featurecounts/WT_REP2.featureCounts.txt.summary").name ).match("hisat2/featurecounts") }, { assert snapshot( // These files are not stable @@ -177,9 +178,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram.txt"), @@ -187,15 +185,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -218,7 +210,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, @@ -230,14 +225,20 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_genome_result.names.txt"), + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annot.nameation_junctions_plot_Events.txt"), file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, @@ -271,15 +272,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -380,12 +375,18 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/salmon_plot.png").name, @@ -478,117 +479,72 @@ nextflow_pipeline { path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/hisat2/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/hisat2/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/hisat2/qualimap/WT_REP2/rnaseq_qc_results.txt"), - // HTML reports are not stable + // HTML reports and these files are not stable + file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/hisat2/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/hisat2/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/hisat2/qualimap/WT_REP2/qualimapReport.html").name + file("${params.outdir}/hisat2/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/hisat2/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/hisat2/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/hisat2/qualimap/WT_REP2/rnaseq_qc_results.txt").name ).match("hisat2/qualimap") }, { assert snapshot( - path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), - path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), - path("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), - path("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP1.bam_stat.txt"), - path("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP2.bam_stat.txt"), path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), path("${params.outdir}/hisat2/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/hisat2/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), - path("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), - path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), - path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), - path("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), - path("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP1.read_distribution.txt"), - path("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP2.read_distribution.txt"), - path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), - path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), - path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), - path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), - path("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), - path("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), - // PDFs and R scripts are not stable + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/hisat2/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/hisat2/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, @@ -604,6 +560,21 @@ nextflow_pipeline { file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, file("${params.outdir}/hisat2/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, @@ -614,6 +585,16 @@ nextflow_pipeline { file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/hisat2/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, @@ -624,43 +605,64 @@ nextflow_pipeline { file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/hisat2/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/hisat2/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/hisat2/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + file("${params.outdir}/hisat2/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("hisat2/rseqc") }, { assert snapshot( path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat"), path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats") + // These files are not stable + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("hisat2/samtools_stats") }, { assert snapshot( path("${params.outdir}/hisat2/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 4c0e4e4fd..2c6a78ff4 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -252,29 +252,29 @@ "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,079b099e5c5e9fe5e2559dfc938aa48b", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,eedff929765dbc950528ee499e6d63ba", - "RAP1_IAA_30M_REP1.featureCounts.txt.summary:md5,b4fd537569e939435344a6c9436bcd85", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,4d1820a35481f454f17a14326356253d", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,b007abbc78b08d8d2bb37a267665947d", - "RAP1_UNINDUCED_REP1.featureCounts.txt.summary:md5,d11369e773d95fe3024cdba224532825", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,3632da2126cb33391428ba0d6d10787f", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,ea897231d1c447d8e395716741b876ab", - "RAP1_UNINDUCED_REP2.featureCounts.txt.summary:md5,c8967f02a4598b23d5f56eaed2a35932", "WT_REP1.biotype_counts_mqc.tsv:md5,abc303e93390bb5bd8f916f8f5978de3", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,39721c0d981304996438bc2f505bf98c", - "WT_REP1.featureCounts.txt.summary:md5,ce8e697f77ca90f65719ba2037c1c107", "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c", - "WT_REP2.featureCounts.txt.summary:md5,48d1f61e21dc37b5206f909606996576" + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.featureCounts.txt.summary", + "WT_REP2.featureCounts.txt.summary" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:35:11.708452" + "timestamp": "2024-08-26T12:58:36.389406" }, "hisat2/samtools_stats": { "content": [ @@ -359,16 +359,16 @@ }, "hisat2/bigwig": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig:md5,c9ae036650d73b275dfa1348c17fb773", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,b00167c81cf99d088ef36cfbe73dd4c0", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,5bafde76df98023212350e1d0c77ee97", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,eb5ecce02b6b206e9970070c4e1dad22", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,c49afa16b0e2be87a043ceb45fd6b13b", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,40916b3a8a8bc183795573ed5014f5f2", - "WT_REP1.forward.bigWig:md5,bd0a7dbda673cada114ab2f5609faae6", - "WT_REP1.reverse.bigWig:md5,b41fa148408c0969f53886d66236f844", - "WT_REP2.forward.bigWig:md5,82a8fec707b818bc18c3861ebd84b3e5", - "WT_REP2.reverse.bigWig:md5,d8ac1d7c396be5c4d36919de64505d4f" + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig", + "WT_REP1.forward.bigWig", + "WT_REP1.reverse.bigWig", + "WT_REP2.forward.bigWig", + "WT_REP2.reverse.bigWig" ], "meta": { "nf-test": "0.9.0", diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index ab2865393..208425695 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -96,9 +96,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), @@ -106,15 +103,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -128,7 +119,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, @@ -147,14 +141,20 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, @@ -191,15 +191,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -295,6 +289,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, @@ -479,12 +479,13 @@ nextflow_pipeline { file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name ).match("salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig") + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), @@ -522,15 +523,15 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary") + file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name ).match("star_salmon/featurecounts") }, { assert snapshot( path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), @@ -565,93 +566,93 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), - // HTML reports are not stable + // HTML reports and these files are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name ).match("star_salmon/qualimap") }, { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), - // PDFs and R scripts are not stable + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name ).match("star_salmon/rseqc") }, { assert snapshot( // These files are not stable @@ -671,28 +672,29 @@ nextflow_pipeline { { assert snapshot( path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), @@ -787,7 +789,7 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon") }, + ).match("star_salmon/salmon_quant") }, { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index da7d1d41f..242c9522c 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -28,6 +28,71 @@ }, "timestamp": "2024-08-23T16:36:12.254374" }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,f9a605d54a0a103566f7a9b8e0867a73", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8f97be8af4e47cc48650c62227a40203", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,a044fe7a3ad445c9a91a0d54ab5015d1", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,7a8ea02d74058efb801e8c62bca96fd4", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,543a047a549437026a1363ea8ddf5b03", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T16:36:12.647521" + }, "trimgalore": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", @@ -47,65 +112,65 @@ }, "star_salmon/rseqc": { "content": [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d00442929f8a18945d4597167fe3bb6d", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,447c12933610cb3e0aeb4560906332c6", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", - "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", - "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", - "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", - "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", - "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", - "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", - "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", - "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", - "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", - "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", - "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", - "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", - "RAP1_IAA_30M_REP1.junction.xls:md5,ce9d38109ceabb83e1349cc1a8779e3f", - "RAP1_UNINDUCED_REP1.junction.xls:md5,34204ec2f7648de90070ec9687c05cb2", - "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,a181a8045a4aaee911e6acd60cc25d43", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,1d91e11972e9b0a55035f4d9b2fa9b86", - 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"samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -284,6 +343,12 @@ "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", "rseqc_bam_stat.png", + "qualimap_genomic_origin-cnt.png", + "qualimap_genomic_origin-pct.png", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png", + "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_saturation_plot_All_Junctions.png", @@ -378,7 +443,38 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T17:12:47.723706" + "timestamp": "2024-08-26T13:06:36.880437" + }, + "Params: --min_mapped_reads 90 - stub": { + "content": [ + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, 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"multiqc_rseqc_junction_annotation.txt:md5,eaf292e3d11398a65903f46365f763be", - "multiqc_rseqc_read_distribution.txt:md5,52dfe8e95ffb71406c321f06f757bfde", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_deduplication.txt:md5,bcf1670f90e552256db4de7fa65d5306", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -614,15 +642,9 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,6d377444d29c3d4135980982ab1df2fb", "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008", - "qualimap_genomic_origin.txt:md5,76988d0ce871eb7190b916bbc4dd5387", "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee", - "qualimap_rnaseq_genome_results.txt:md5,dbaf0e70a31c7606afb2c8b758693d6d", - "rseqc_bam_stat.txt:md5,b468d3e451b9f20b02653df836e56ab7", "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,7d52ed0ea2a109428249cc835c64fd7f", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,b4d76efb9fe0c30418b78dd6c61c42fa", - "rseqc_read_distribution_plot.txt:md5,27c914f0530d633c860da6eccba18515", - "rseqc_read_dups_plot.txt:md5,54f7e9aae54c41b712da0a1588e3140f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -635,7 +657,10 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", + "multiqc_rseqc_junction_annotation.txt", + "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -654,14 +679,20 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "qualimap_genomic_origin.txt", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", @@ -673,7 +704,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T17:12:47.537212" + "timestamp": "2024-08-26T13:06:36.810224" }, "star_salmon/deseq2_qc": { "content": [ @@ -715,21 +746,21 @@ "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f3688a214d33a43ad79abe4b31df0c4b", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,b38da3230d4d29ebc8d4af36852d7212", - "RAP1_IAA_30M_REP1.featureCounts.txt.summary:md5,350e320b341a252ecfb569d4f412a02e", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,d241d50e582ceb97e6f16b3556f5f5a9", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,2ab175746532de1c54020c1eabc27bb5", - "RAP1_UNINDUCED_REP1.featureCounts.txt.summary:md5,2b834f8b69c28d80ccfc51440bc693ff", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,b621ce1e803d8670ece6c66391c33ba4", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,480b2586a878bc22f5b73f94051b41d8", - "RAP1_UNINDUCED_REP2.featureCounts.txt.summary:md5,1c69f066c7457c2633f4f90f322744fc" + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.featureCounts.txt.summary" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T16:36:12.226089" + "timestamp": "2024-08-26T13:06:36.957812" }, "salmon/deseq2_qc": { "content": [ @@ -808,12 +839,12 @@ }, "star_salmon/bigwig": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig:md5,0abafd7a9f9035469c003fd3dabd73e8", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,0f1e9ac71fc0b99785f06ecb860ef00e", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,09e8d65e21ac92e9a3b78afe3acdf28b", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,8b002d23911f95f1c5b9965c2e7d0737", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,eede9cac23d47c4685dc13507e97bfb9", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,a835e0ac51231016c52de94c18ebd466" + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig" ], "meta": { "nf-test": "0.9.0", @@ -899,72 +930,41 @@ "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", - "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", - "Reads Genomic Origin.png:md5,477fbfe923c7d416b507fb488f659ba9", "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", - "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", - "Reads Genomic Origin.png:md5,e19e85335cf6f64495f4691f15cf39d8", "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", "Coverage Profile Along Genes (Low).png:md5,b6adc296e9a732aa0495a6da8fa4ed90", "Coverage Profile Along Genes (Total).png:md5,fcb94fb9c1a51c1db32f884d05929cc8", - "Junction Analysis.png:md5,39ac823182971b41faec683b981cfcfa", - "Reads Genomic Origin.png:md5,1c0624213e8627aa2496d045117a4fe8", "Transcript coverage histogram.png:md5,3aeb52ff3e3752727a370b0d7ceb0518", "coverage_profile_along_genes_(high).txt:md5,3b20a736708df02ea8c86dc5829ae67e", "coverage_profile_along_genes_(low).txt:md5,02b314b76ef1317f20e129412340755d", "coverage_profile_along_genes_(total).txt:md5,02b314b76ef1317f20e129412340755d", - "rnaseq_qc_results.txt:md5,3eed764ef657161586b04670aad512d6", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", - "qualimapReport.html" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T16:36:12.305856" - }, - "Params: --min_mapped_reads 90 - stub": { - "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", - "genome_transcriptome.fasta", - "genome_transcriptome.gtf", - "RAP1_IAA_30M_REP1_raw.html", - "RAP1_IAA_30M_REP1_raw.zip", - "RAP1_UNINDUCED_REP1_raw.html", - "RAP1_UNINDUCED_REP1_raw.zip", - "RAP1_UNINDUCED_REP2_raw.html", - "RAP1_UNINDUCED_REP2_raw.zip", - "WT_REP1_raw.html", - "WT_REP1_raw.zip", - "WT_REP2_raw.html", - "WT_REP2_raw.zip", - "multiqc_report.html", - "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt", - "RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP1_trimmed_2.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_1.fastq.gz_trimming_report.txt", - "WT_REP2_trimmed_2.fastq.gz_trimming_report.txt" + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T16:57:32.155191" + "timestamp": "2024-08-26T13:06:37.041504" } -} +} \ No newline at end of file diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 1242c1fbe..4acb69a7e 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -95,9 +95,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), @@ -105,15 +102,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -127,6 +118,15 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, @@ -191,15 +191,9 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -297,12 +291,18 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, @@ -491,16 +491,17 @@ nextflow_pipeline { file("${params.outdir}/sortmerna/WT_REP2.sortmerna.log").name ).match("star_salmon/sortmerna") }, { assert snapshot( - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig"), - path("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig") + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name ).match("star_salmon/bigwig") }, { assert snapshot( path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), @@ -548,23 +549,23 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), - path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary") + file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name ).match("star_salmon/featurecounts") }, { assert snapshot( path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), @@ -601,117 +602,72 @@ nextflow_pipeline { path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), - path("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt"), - // HTML reports are not stable + // HTML reports and these files are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, - file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name + file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name ).match("star_salmon/qualimap") }, { assert snapshot( - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt"), - path("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls"), - path("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls"), - // PDFs and R scripts are not stable + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, @@ -727,6 +683,21 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, @@ -737,6 +708,16 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, @@ -747,11 +728,31 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, - file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("star_salmon/rseqc") }, { assert snapshot( // These files are not stable @@ -771,34 +772,35 @@ nextflow_pipeline { { assert snapshot( path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats") + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), @@ -913,7 +915,7 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name - ).match("star_salmon") }, + ).match("star_salmon/salmon_quant") }, { assert snapshot( // These reports are not stable file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 0d0ef618a..0199ff877 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -28,6 +28,71 @@ }, "timestamp": "2024-08-23T18:00:12.426991" }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", + "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", + "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", + "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", + "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", + "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", + "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf", + "fld.gz", + "meta_info.json", + "flenDist.txt", + "salmon_quant.log", + "quant.genes.sf", + "quant.sf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-23T18:00:13.580621" + }, "trimgalore": { "content": [ "RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt", @@ -47,61 +112,16 @@ }, "star_salmon/rseqc": { "content": [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,4256d7f43715daff481bf0010b695981", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d04cb03c42168319cb306f0b866b6b59", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,5e114cb96f02f9fadd21e2a9826a68a6", - "WT_REP1.bam_stat.txt:md5,bc6521a8455de55571a3ae6ef5a07aa2", - "WT_REP2.bam_stat.txt:md5,22fd302c0f8ab19b114caa4b8d47a92c", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,ee69422d6e76fba223aa6b20a13027d2", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,ec9ec42ddfd3ffbb5373d3d6b6713b2c", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,484e2860c6c496b1da5fac475a0cd3e4", "WT_REP1.infer_experiment.txt:md5,298c430c61cb7a46b48af867a0dfe00b", "WT_REP2.infer_experiment.txt:md5,18758f433cf5c19bce599e5329da39a9", - "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", - "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", - "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", - "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", - "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", - "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", - "WT_REP1.junction.Interact.bed:md5,2132b64829f397caeb41b3b4eaa8eadf", - "WT_REP1.junction.bed:md5,f9214aec5c178ffae736308615d2535e", - "WT_REP2.junction.Interact.bed:md5,0da2295d05c6a5de213c2172350ba87e", - "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", - "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", - "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", - "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", - "WT_REP1.junction_annotation.log:md5,e26d4111fd4e731a9f2a10fcadee9090", - "WT_REP2.junction_annotation.log:md5,1b95af725477bbe771ed4e7b7d693729", - "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", - "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", - "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", - "WT_REP1.junction_plot.r:md5,3a6e7f258151c69d3472d7ac3afe19f1", - "WT_REP2.junction_plot.r:md5,146b3da40cd5944c3eabc6e948fd8e44", - "RAP1_IAA_30M_REP1.junction.xls:md5,ce9d38109ceabb83e1349cc1a8779e3f", - "RAP1_UNINDUCED_REP1.junction.xls:md5,34204ec2f7648de90070ec9687c05cb2", - "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", - "WT_REP1.junction.xls:md5,d25b37752ce12695ef08c2842a0c01b1", - "WT_REP2.junction.xls:md5,1a3c7d9a4ac9159b87caa1f4ef4b6748", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,37fadf8a5d3e6d4276fdcc217a0df8ab", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,ac45c5dfa40382fd2613c85754dde373", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,de16f30d41f987f875e880bd3356d3f0", - "WT_REP1.read_distribution.txt:md5,b72fac25d0cf554a657029290ca20bdd", - "WT_REP2.read_distribution.txt:md5,9042fc9da71efb3f68ab254088dcba54", - "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,afe0a648fafb80250e6d67865bbbfc3f", - "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,e900364ed504bfb704295345471e39ed", - "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,6b3800c7ee5d1b873fa9c1f5ddfa3449", - "WT_REP1.DupRate_plot.r:md5,99bcfa0636316c8681a80b284a733867", - "WT_REP2.DupRate_plot.r:md5,9e531ac620795015672007456755a90f", - "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,825f80662e5525c3303fc63b741e908c", - "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,e54f45dcc2e2cdebcd86602dbf938538", - "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,73c39a8c11fa0b1c94025942ca9d5d41", - "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,80e5b2b1ce48edc1c6a7deeff69f5fce", - "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,d3aa129590e9fec24c01c39f09f7e734", - "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,5f017f8cd9b254daeeae0b5e7b74bed7", - "WT_REP1.pos.DupRate.xls:md5,f1ce288eec6e9ad760c6499cfe9e6ff9", - "WT_REP1.seq.DupRate.xls:md5,7e1b37c441fa9d05d584931ec5d7042f", - "WT_REP2.pos.DupRate.xls:md5,bba919e65f7001299bda2980da0e08a9", - "WT_REP2.seq.DupRate.xls:md5,9b15bcb5b3634f8dfe177e859ee40582", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP2.bam_stat.txt", + "WT_REP1.bam_stat.txt", + "WT_REP2.bam_stat.txt", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", "WT_REP1.inner_distance_plot.pdf", "WT_REP2.inner_distance_plot.pdf", @@ -117,6 +137,21 @@ "WT_REP2.inner_distance.txt", "WT_REP2.inner_distance_freq.txt", "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_UNINDUCED_REP1.junction.Interact.bed", + "RAP1_UNINDUCED_REP1.junction.bed", + "RAP1_UNINDUCED_REP2.junction.Interact.bed", + "RAP1_UNINDUCED_REP2.junction.bed", + "WT_REP1.junction.Interact.bed", + "WT_REP1.junction.bed", + "WT_REP2.junction.Interact.bed", + "WT_REP2.junction.bed", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP2.junction_annotation.log", + "WT_REP1.junction_annotation.log", + "WT_REP2.junction_annotation.log", "RAP1_IAA_30M_REP1.splice_events.pdf", "RAP1_IAA_30M_REP1.splice_junction.pdf", "RAP1_UNINDUCED_REP1.splice_events.pdf", @@ -127,6 +162,16 @@ "WT_REP1.splice_junction.pdf", "WT_REP2.splice_events.pdf", "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP2.junction_plot.r", + "WT_REP1.junction_plot.r", + "WT_REP2.junction_plot.r", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_UNINDUCED_REP1.junction.xls", + "RAP1_UNINDUCED_REP2.junction.xls", + "WT_REP1.junction.xls", + "WT_REP2.junction.xls", "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", @@ -137,17 +182,37 @@ "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", "WT_REP1.junctionSaturation_plot.r", "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP2.read_distribution.txt", + "WT_REP1.read_distribution.txt", + "WT_REP2.read_distribution.txt", "RAP1_IAA_30M_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", "WT_REP1.DupRate_plot.pdf", - "WT_REP2.DupRate_plot.pdf" + "WT_REP2.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP2.DupRate_plot.r", + "WT_REP1.DupRate_plot.r", + "WT_REP2.DupRate_plot.r", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "WT_REP1.pos.DupRate.xls", + "WT_REP1.seq.DupRate.xls", + "WT_REP2.pos.DupRate.xls", + "WT_REP2.seq.DupRate.xls" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:00:12.964807" + "timestamp": "2024-08-26T13:19:36.262464" }, "references": { "content": [ @@ -164,40 +229,40 @@ "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,9cb85f4008ba88f43e15fae47baad525", "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats:md5,30a151b6c5b3e97ba1ce11f5d05f932c", "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,8ac0db45c52a28d167582874992e5833", "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_IAA_30M_REP1.sorted.bam.stats:md5,d4c6d89bd5535a1b6f5da146afae7d2a", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,0496e26c6be67b341255761a447b1569", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats:md5,ac026df38190e6396ac8b56d010003cc", "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,12fb0d3b2c65e4738f30d530a329efb1", "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP1.sorted.bam.stats:md5,fb6df04fadbc0e0217fcf698f629a6ab", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,2df8940452346d9d82b95206d4b304e1", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats:md5,39b06485aa392287babe082461ce867d", "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,3535e1cbe40f90e3749dad930251dd9f", "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "RAP1_UNINDUCED_REP2.sorted.bam.stats:md5,b294e517e7bb2b834f3eb4c79fb23175", "WT_REP1.markdup.sorted.bam.flagstat:md5,d931e8e7fd82c493d12e78f404b13f2c", "WT_REP1.markdup.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP1.markdup.sorted.bam.stats:md5,eab9ca07ab0146b8006f3dbbe54d5e80", "WT_REP1.sorted.bam.flagstat:md5,7bffb4d7dff374febb1ca99c1436ebf7", "WT_REP1.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP1.sorted.bam.stats:md5,b8c51656e1e51bb8346e7e5a7705e516", "WT_REP2.markdup.sorted.bam.flagstat:md5,ca4330f24cf0d98ceb18c617294aed9e", "WT_REP2.markdup.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", - "WT_REP2.markdup.sorted.bam.stats:md5,91c051ad91cc1390bc7f1e3a96a2a4e4", "WT_REP2.sorted.bam.flagstat:md5,41d560c31aa88088efffe62d0f488583", "WT_REP2.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", - "WT_REP2.sorted.bam.stats:md5,f1a410cbbacb0e0ee9b441ee13635909" + "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:00:13.24168" + "timestamp": "2024-08-26T13:19:36.4571" }, "multiqc_plots": { "content": [ @@ -228,15 +293,9 @@ "picard_deduplication-pct.png:md5,73b0c4736e772c7daeae10f09dd73d21", "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598", "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00", - "qualimap_genomic_origin-cnt.png:md5,6a8f85d22eebf8accb1189c2c6117e98", - "qualimap_genomic_origin-pct.png:md5,21cf447eab8ac7c76ec99365bd26f6c6", "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa", - "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,2c571e9a5bb9a7df26bbe00e0c18fbb2", - "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,b32557abbcd5673e5aad9c31382d36f6", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,02a58fa6112699eb73a10bc62e8ff562", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,ccace8d19fd96e93939c9d446640dc37", - "rseqc_read_distribution_plot-cnt.png:md5,b2829f6aa6980132546b37245c93cec1", - "rseqc_read_distribution_plot-pct.png:md5,dc04a26174a9d9f3c778c5ffd4041d7a", "rseqc_read_dups_plot.png:md5,1a18ce4ca5f36722f1fdd579d7eb41e1", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -333,12 +392,18 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "qualimap_genomic_origin-cnt.png", + "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png", + "rseqc_junction_annotation_junctions_plot_Events-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", @@ -429,7 +494,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:00:10.868338" + "timestamp": "2024-08-26T13:19:35.873754" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -536,71 +601,6 @@ }, "timestamp": "2024-08-23T18:00:13.357765" }, - "star_salmon": { - "content": [ - "ambig_info.tsv:md5,6cd02367152bb2dd59a6f1f70df2d7f8", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,4cc2492f557e5e0a2911a0bd83a51020", - "ambig_info.tsv:md5,8611b6c03f6aa1a5f3dfceb0e65ad4ef", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,dc750c3564c63da54979c852794d58a5", - "ambig_info.tsv:md5,1b69f9b651dfa6799e310004c1e3309f", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,db43ed650e6e7b42cd2c5b8101bb6748", - "ambig_info.tsv:md5,070c7d50eab5ce0f211cdb06f9d7cc29", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,e418b4e899623449c6babdf53e5aabde", - "ambig_info.tsv:md5,b8c61854b56a1c9a0fc8f158ea0c7599", - "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", - "observed_bias.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "observed_bias_3p.gz:md5,92bcd0592d22a6a58d0360fc76103e56", - "cmd_info.json:md5,f234c8d322df3b59d990594c63b24eae", - "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf", - "fld.gz", - "meta_info.json", - "flenDist.txt", - "salmon_quant.log", - "quant.genes.sf", - "quant.sf" - ], - "meta": { - "nf-test": "0.9.0", - "nextflow": "24.04.4" - }, - "timestamp": "2024-08-23T18:00:13.580621" - }, "salmon_quant": { "content": [ "ambig_info.tsv:md5,25ced9693254994a7878241225baabb6", @@ -701,9 +701,6 @@ "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", "multiqc_picard_dups.txt:md5,5e93e7e4ecaeed2550bffa44dc32184b", - "multiqc_rseqc_bam_stat.txt:md5,e4408b581842f3458e1b4efcdd178bc0", - "multiqc_rseqc_junction_annotation.txt:md5,e67493668e9b93f6e15c145d8d844372", - "multiqc_rseqc_read_distribution.txt:md5,0132183561c399a5b57eee5f82bda19e", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", "picard_deduplication.txt:md5,32d912bd78e7d99276a52e13575d08aa", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -711,15 +708,9 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,50e9209baeaafe181ce3b5caa05cf789", "qualimap_gene_coverage_profile_Normalised.txt:md5,6ed32f112c679e73396350cbe5cb9459", - "qualimap_genomic_origin.txt:md5,d0c0d1c67bfaa14dbdd7ded00ece8565", "qualimap_rnaseq_cov_hist.txt:md5,a895b3af229f661da1edbc21ec72edaa", - "qualimap_rnaseq_genome_results.txt:md5,b894c46e703a343da6d69ee55599c727", - "rseqc_bam_stat.txt:md5,7a35d200db642e6b0ea269a8f934b345", "rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,1dfd3130b0f3a45541ef15fd2525d044", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,f4aa74934a4c73c2c8a1b78866090419", - "rseqc_read_distribution_plot.txt:md5,c9a534adc9cf9c1856712c04490a6303", - "rseqc_read_dups_plot.txt:md5,deac8cf2fb64d0a6a218522426f0d6e9", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", @@ -732,6 +723,15 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_rseqc_bam_stat.txt", + "multiqc_rseqc_junction_annotation.txt", + "multiqc_rseqc_read_distribution.txt", + "qualimap_genomic_origin.txt", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_read_distribution_plot.txt", + "rseqc_read_dups_plot.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", @@ -772,7 +772,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T10:39:39.81199" + "timestamp": "2024-08-26T13:19:35.782125" }, "star_salmon/deseq2_qc": { "content": [ @@ -818,29 +818,29 @@ "RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv:md5,f36792d25b268b6d556f8728300f4afc", "RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv:md5,dde2de0cb90e10d0195c726f768e9941", "RAP1_IAA_30M_REP1.featureCounts.txt:md5,c5865ded7168476d93057d2aedaec694", - "RAP1_IAA_30M_REP1.featureCounts.txt.summary:md5,e63d83b8018e29fbd8cbf584fb54ee0a", "RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv:md5,782f5001d411ba79314ba77f7d36b157", "RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv:md5,845ff9059c72bc6722a8de69776e22bb", "RAP1_UNINDUCED_REP1.featureCounts.txt:md5,a0fb30c2b937a5a41ac865ab09367af7", - "RAP1_UNINDUCED_REP1.featureCounts.txt.summary:md5,dc54d685d267cd6ae8ec607407f8c631", "RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv:md5,1c9d07d9f9d12219d2b9f761f854eced", "RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv:md5,6d3fa4c88c7fe61f638e4624ad5e22f0", "RAP1_UNINDUCED_REP2.featureCounts.txt:md5,de016e691f5d56b13bbaa626ce2cc93e", - "RAP1_UNINDUCED_REP2.featureCounts.txt.summary:md5,7b389e1f707eb19947f8bbe5f179b4e7", "WT_REP1.biotype_counts_mqc.tsv:md5,eca4a76b9243248d01df5f4289b8201e", "WT_REP1.biotype_counts_rrna_mqc.tsv:md5,8ef76d717492ca23764938aee8ea33a9", "WT_REP1.featureCounts.txt:md5,7aadafd0a26f5047a9ae7266eccfce05", - "WT_REP1.featureCounts.txt.summary:md5,e47cd71f04be7b8f80ea9d0596c3109f", "WT_REP2.biotype_counts_mqc.tsv:md5,530605b80da27915a90d452249f3243a", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,809af01851125c401d576c21efca7b5a", - "WT_REP2.featureCounts.txt.summary:md5,f335eeffd8e609abf9cb695a939e8adf" + "RAP1_IAA_30M_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP1.featureCounts.txt.summary", + "RAP1_UNINDUCED_REP2.featureCounts.txt.summary", + "WT_REP1.featureCounts.txt.summary", + "WT_REP2.featureCounts.txt.summary" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:00:12.260982" + "timestamp": "2024-08-26T13:19:35.982363" }, "salmon/deseq2_qc": { "content": [ @@ -921,16 +921,16 @@ }, "star_salmon/bigwig": { "content": [ - "RAP1_IAA_30M_REP1.forward.bigWig:md5,fed2e9026362a9d05245b17358c8d7f6", - "RAP1_IAA_30M_REP1.reverse.bigWig:md5,3f792ce1bbb5150ebdca9cc6ba3d624b", - "RAP1_UNINDUCED_REP1.forward.bigWig:md5,00de9f9cb68295cfa4aed0140d961675", - "RAP1_UNINDUCED_REP1.reverse.bigWig:md5,b0a67389e984cb0ab53a6a1f0188ba4f", - "RAP1_UNINDUCED_REP2.forward.bigWig:md5,ecaa5e602147059501f441f7c7b7f9c2", - "RAP1_UNINDUCED_REP2.reverse.bigWig:md5,17bb3e8ae1093e8f34c75958bb241340", - "WT_REP1.forward.bigWig:md5,ed5809ec296692ef211470d89b5af880", - "WT_REP1.reverse.bigWig:md5,6101b00105e45858d498156b0375f2ac", - "WT_REP2.forward.bigWig:md5,f76eb87eca6c4bcb7c2e1f1a705f27e7", - "WT_REP2.reverse.bigWig:md5,c773770995dd4c31fbbec065bc67e72f" + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig", + "WT_REP1.forward.bigWig", + "WT_REP1.reverse.bigWig", + "WT_REP2.forward.bigWig", + "WT_REP2.reverse.bigWig" ], "meta": { "nf-test": "0.9.0", @@ -1040,63 +1040,63 @@ "Coverage Profile Along Genes (High).png:md5,1a837e43161d7133e9156c7b18123aa9", "Coverage Profile Along Genes (Low).png:md5,46c5ba09af49602b956efd780f7a39e4", "Coverage Profile Along Genes (Total).png:md5,b04cac9c2d15b1b9623d87d44caadff6", - "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", - "Reads Genomic Origin.png:md5,4e658a8fd5b6c6939f5bf3e459332bae", "Transcript coverage histogram.png:md5,cbb250c6903bfe6ecab5fb4b2ca661e5", "coverage_profile_along_genes_(high).txt:md5,5aee6c959137a8c9bfbd0ddaa79dddba", "coverage_profile_along_genes_(low).txt:md5,d2742410803e0de7cc606ef118010ea8", "coverage_profile_along_genes_(total).txt:md5,d2742410803e0de7cc606ef118010ea8", - "rnaseq_qc_results.txt:md5,7c902840996e1c660446122723e838e1", "Coverage Profile Along Genes (High).png:md5,8c8b46f9bfb6cf952a95d85a6b917444", "Coverage Profile Along Genes (Low).png:md5,5c56671f085c6db7fd86b41bb5b7e6d0", "Coverage Profile Along Genes (Total).png:md5,b83fbaedfe4dcfdd7b3970d2ff27d517", - "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", - "Reads Genomic 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"coverage_profile_along_genes_(low).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", "coverage_profile_along_genes_(total).txt:md5,db2e0acbe9f07c68bcd7e08e036f02d3", - "rnaseq_qc_results.txt:md5,ec01623528b9eb3e11547262f1f72ad9", "Coverage Profile Along Genes (High).png:md5,d8a36870a6f262c41995b4b5bd26a149", "Coverage Profile Along Genes (Low).png:md5,5570af90ee685a3c95117519aa6bdc46", "Coverage Profile Along Genes (Total).png:md5,eb53e699213ce453cbea7f71f5204b08", - "Junction Analysis.png:md5,61860303f0b3661cf45f834b347485e2", - "Reads Genomic Origin.png:md5,5b60ad1524d485fb509f42ae90c71f41", "Transcript coverage histogram.png:md5,f0bd8d82a8b7adec6e1f1ef85633eded", "coverage_profile_along_genes_(high).txt:md5,a349232d75f6c0adab6afcd9f6cbbafb", "coverage_profile_along_genes_(low).txt:md5,b2c696661e6c524b1641eb7267c70edc", "coverage_profile_along_genes_(total).txt:md5,b2c696661e6c524b1641eb7267c70edc", - "rnaseq_qc_results.txt:md5,84879fb36ed25857057d6c454a53b8f0", "Coverage Profile Along Genes (High).png:md5,3c1c603d63f3f7f9ba1ab6e7749b7771", "Coverage Profile Along Genes (Low).png:md5,9f80251ed043cf900fa939cc254ccc81", "Coverage Profile Along Genes (Total).png:md5,a420f287f986a8db317be712ac0a2237", - "Junction Analysis.png:md5,147d7341869d7446ae0ad4dd1e3de700", - "Reads Genomic Origin.png:md5,b670a984779e0edd5b80599e97868812", "Transcript coverage histogram.png:md5,c467c5eac12a95f8569198927434440d", "coverage_profile_along_genes_(high).txt:md5,3f76529bd723d5320c86cc407fbb3294", "coverage_profile_along_genes_(low).txt:md5,b9be191fdec82c78057e083d3adf20dd", "coverage_profile_along_genes_(total).txt:md5,b9be191fdec82c78057e083d3adf20dd", - "rnaseq_qc_results.txt:md5,3f9f5d5acac942709d114bf3db75baa2", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", - "qualimapReport.html" + "rnaseq_qc_results.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T18:00:12.786569" + "timestamp": "2024-08-26T13:19:36.107982" } } \ No newline at end of file diff --git a/tests/salmon.nf.test.snap b/tests/salmon.nf.test.snap index 356d970b3..6865c5f3c 100644 --- a/tests/salmon.nf.test.snap +++ b/tests/salmon.nf.test.snap @@ -265,7 +265,7 @@ }, "Params: --pseudo_aligner salmon --skip_qc --skip_alignment - stub": { "content": [ - "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, FASTQC={fastqc=0.12.1}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, STAR_GENOMEGENERATE={star=2.7.10a, samtools=1.18, gawk=5.1.0}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", + "{BBMAP_BBSPLIT={bbmap=39.01}, CAT_FASTQ={cat=8.3}, CUSTOM_CATADDITIONALFASTA={python=null}, CUSTOM_GETCHROMSIZES={getchromsizes=1.2}, GTF2BED={perl=5.26.2}, GTF_FILTER={python=3.9.5}, GUNZIP_ADDITIONAL_FASTA={gunzip=1.1}, GUNZIP_GTF={gunzip=1.1}, TRIMGALORE={trimgalore=0.6.7, cutadapt=3.4}, UNTAR_SALMON_INDEX={untar=1.34}, Workflow={nf-core/rnaseq=v3.15.0dev}}", "genome_transcriptome.fasta", "genome_transcriptome.gtf", "RAP1_IAA_30M_REP1_raw.html", From 439ae75b47c94de5e4cc6aa8727c0eb79e79b0ed Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 14:20:12 +0200 Subject: [PATCH 34/41] fix tests and snapshots --- tests/featurecounts_group_type.nf.test | 2 +- tests/featurecounts_group_type.nf.test.snap | 174 +++++++++--------- tests/hisat2.nf.test | 3 +- tests/hisat2.nf.test.snap | 193 ++++++++++---------- 4 files changed, 185 insertions(+), 187 deletions(-) diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 4d79c7ae8..9ec8f1aa6 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -285,7 +285,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctio.namens_plot_Events-cnt.png"), + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 3c11ea4c9..6c136b14e 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -213,61 +213,16 @@ }, "star_salmon/rseqc": { "content": [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b882e444c89be4ceed80e29865166b1a", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,d00442929f8a18945d4597167fe3bb6d", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,447c12933610cb3e0aeb4560906332c6", - "WT_REP1.bam_stat.txt:md5,85d14e5c3943407e636186424fd766cb", - "WT_REP2.bam_stat.txt:md5,12ae5d98f3e5cf7b3a70eed45f12cbe2", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,169d25b95c008bebe9ce886fea6a4e33", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,2ca0ce0fd3204bd2cc4812c4655b1f1f", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,7d5705880188f9beab1939e08d6b8f40", "WT_REP1.infer_experiment.txt:md5,bf0c137f5fca06e7c40e1984a1acb06d", "WT_REP2.infer_experiment.txt:md5,82e23b329ee60709f343bc2d17d43b14", - "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,71af7df839b494ea12df802369befb06", - "RAP1_IAA_30M_REP1.junction.bed:md5,abc741dcce71900d4145f3aaf3bd9c64", - "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,228588b36cef3af0c46e1c819e801931", - "RAP1_UNINDUCED_REP1.junction.bed:md5,ce6b9b387adbad82a9bf798d07e65b15", - "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,6785b859d1e06d30b3939d7f95050364", - "RAP1_UNINDUCED_REP2.junction.bed:md5,112233f4d8b6c929e1b7d5ef74556436", - "WT_REP1.junction.Interact.bed:md5,a989d63b778be8daa2df6ea57ac3fc93", - "WT_REP1.junction.bed:md5,a0082fba0e4222d41fc5e5c6ba6db453", - "WT_REP2.junction.Interact.bed:md5,0da2295d05c6a5de213c2172350ba87e", - "WT_REP2.junction.bed:md5,0b01bf3d08378094bc063f123ed201d4", - "RAP1_IAA_30M_REP1.junction_annotation.log:md5,0c83bfd72c550d18a389ffebfb7549fc", - "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,62db928876d7cc95d17882ef7d7d72ab", - "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,b9e6c428934326fc8f86445ba0cea4c8", - "WT_REP1.junction_annotation.log:md5,93ff20da87153de88c5686588330abd2", - "WT_REP2.junction_annotation.log:md5,1b95af725477bbe771ed4e7b7d693729", - "RAP1_IAA_30M_REP1.junction_plot.r:md5,3fac4c9b025b9182a64d307beab3236e", - "RAP1_UNINDUCED_REP1.junction_plot.r:md5,4d8de27e0dc248cebb9daa3f8f6fd50d", - "RAP1_UNINDUCED_REP2.junction_plot.r:md5,252727594fa22dcf4224bdcc057be6b9", - "WT_REP1.junction_plot.r:md5,1ffa6c2df67179c4335fb79db597ad50", - "WT_REP2.junction_plot.r:md5,146b3da40cd5944c3eabc6e948fd8e44", - "RAP1_IAA_30M_REP1.junction.xls:md5,ce9d38109ceabb83e1349cc1a8779e3f", - "RAP1_UNINDUCED_REP1.junction.xls:md5,34204ec2f7648de90070ec9687c05cb2", - "RAP1_UNINDUCED_REP2.junction.xls:md5,2a7801927b9a90c6f832458e458884f4", - "WT_REP1.junction.xls:md5,02119fa98515474e525ea86ddd1b189c", - "WT_REP2.junction.xls:md5,1a3c7d9a4ac9159b87caa1f4ef4b6748", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,a181a8045a4aaee911e6acd60cc25d43", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,1d91e11972e9b0a55035f4d9b2fa9b86", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,ece206e073f3410f6e40d2ff91c9a714", - "WT_REP1.read_distribution.txt:md5,7521690f215bf27fe161b8e6d7c38769", - "WT_REP2.read_distribution.txt:md5,c11d02cba5674017b90c8372abee3e39", - "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,0505b253ebe3a21cb06a04a08c9313dd", - "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,630db79b02077966911b521a1894e1e1", - "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,4c7cbbb403a09b1056591772867977bd", - "WT_REP1.DupRate_plot.r:md5,99e3eac32a2a2b508501c35c1cccd2bc", - "WT_REP2.DupRate_plot.r:md5,c61f96c3761940feed3f60950ef8ac84", - "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,28c98318b0858f06987d3769228dfffb", - "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,8ab97ebe54912525b971bf82f2ff08a6", - "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,01d81e64075b8381f8467cf7b7601ea1", - "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,070f3b1f484e2603fb61ac34bfb531c4", - "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,3ba876c7a04c1c81260f823f0060c7ac", - "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,941ee93c523c226aad6e6304e9c427e7", - "WT_REP1.pos.DupRate.xls:md5,aba7ea30dc35e376f7655ef298fcaf1c", - "WT_REP1.seq.DupRate.xls:md5,44355ee29233ddd150cd9542e807cc1a", - "WT_REP2.pos.DupRate.xls:md5,c683b1637e778113bb0a75843ff290af", - "WT_REP2.seq.DupRate.xls:md5,ab100995d906dcd338ec8f7f8a6d3fe0", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP2.bam_stat.txt", + "WT_REP1.bam_stat.txt", + "WT_REP2.bam_stat.txt", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", "WT_REP1.inner_distance_plot.pdf", "WT_REP2.inner_distance_plot.pdf", @@ -283,6 +238,21 @@ "WT_REP2.inner_distance.txt", "WT_REP2.inner_distance_freq.txt", "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_UNINDUCED_REP1.junction.Interact.bed", + "RAP1_UNINDUCED_REP1.junction.bed", + "RAP1_UNINDUCED_REP2.junction.Interact.bed", + "RAP1_UNINDUCED_REP2.junction.bed", + "WT_REP1.junction.Interact.bed", + "WT_REP1.junction.bed", + "WT_REP2.junction.Interact.bed", + "WT_REP2.junction.bed", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP2.junction_annotation.log", + "WT_REP1.junction_annotation.log", + "WT_REP2.junction_annotation.log", "RAP1_IAA_30M_REP1.splice_events.pdf", "RAP1_IAA_30M_REP1.splice_junction.pdf", "RAP1_UNINDUCED_REP1.splice_events.pdf", @@ -293,6 +263,16 @@ "WT_REP1.splice_junction.pdf", "WT_REP2.splice_events.pdf", "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP2.junction_plot.r", + "WT_REP1.junction_plot.r", + "WT_REP2.junction_plot.r", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_UNINDUCED_REP1.junction.xls", + "RAP1_UNINDUCED_REP2.junction.xls", + "WT_REP1.junction.xls", + "WT_REP2.junction.xls", "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", @@ -303,17 +283,37 @@ "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", "WT_REP1.junctionSaturation_plot.r", "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP2.read_distribution.txt", + "WT_REP1.read_distribution.txt", + "WT_REP2.read_distribution.txt", "RAP1_IAA_30M_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", "WT_REP1.DupRate_plot.pdf", - "WT_REP2.DupRate_plot.pdf" + "WT_REP2.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP2.DupRate_plot.r", + "WT_REP1.DupRate_plot.r", + "WT_REP2.DupRate_plot.r", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "WT_REP1.pos.DupRate.xls", + "WT_REP1.seq.DupRate.xls", + "WT_REP2.pos.DupRate.xls", + "WT_REP2.seq.DupRate.xls" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:43:26.728929" + "timestamp": "2024-08-26T14:18:39.109008" }, "references": { "content": [ @@ -369,40 +369,40 @@ "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats:md5,343fed237246c2fa05448ee35f6ca576", "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.stats:md5,e32e72af9ed78cc2bd7b13f9a346b1ae", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats:md5,670e8e469a04f4f23c6a9e9f618a9fff", "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.stats:md5,0abe3a520e6c91ed95f58f0f0a78315e", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats:md5,2b6cb09b61cf70580facfd19f7830fbc", "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.stats:md5,1f52bfe3684e46e19c6f03d446cfb997", "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.markdup.sorted.bam.stats:md5,cace1fe9ae48456da96b12892a545b75", "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.stats:md5,52589c03e46d86f8d39edd7c05acf11c", "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - 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"qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", - "qualimap_genomic_origin-cnt.png:md5,49c63998f83c3220a35cd4839bf7fecd", - "qualimap_genomic_origin-pct.png:md5,ab6697c27cf430782bda984483e708e9", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,1003e4b5012bbddc40badd9e2dfdda8e", - "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,676644afc0aee6f63c1299b691b2b93f", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,e7636c4fcd19e7b7bb1731ac7e60d7ea", - "rseqc_read_distribution_plot-cnt.png:md5,7940585c2e998d91a608ac48716c4ab1", - "rseqc_read_distribution_plot-pct.png:md5,b6a312b41ed143a7cd8f19a3dd23696d", 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"rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", @@ -664,7 +664,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:34:58.174823" + "timestamp": "2024-08-26T14:18:38.023639" }, "star_salmon/picard_metrics": { "content": [ @@ -982,63 +982,63 @@ "Coverage Profile Along Genes (High).png:md5,876c1b88f33bd3e5fe1a41679729573d", "Coverage Profile Along Genes (Low).png:md5,ee1f2c9cc4dd4867811eda1e68864ab4", "Coverage Profile Along Genes (Total).png:md5,53747a8f9813744902756ad60638380a", - "Junction Analysis.png:md5,f8c86946a4ac6122ea43495081927d85", - "Reads Genomic Origin.png:md5,477fbfe923c7d416b507fb488f659ba9", "Transcript coverage histogram.png:md5,4f9072d4b11216373b59396293803a37", "coverage_profile_along_genes_(high).txt:md5,fcb06d460810c0555de5396b9dae05e8", "coverage_profile_along_genes_(low).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", "coverage_profile_along_genes_(total).txt:md5,e3c9a1ddfdb89f8534ff7548b70fce32", - "rnaseq_qc_results.txt:md5,fdf42ac95316d03a8ed66ab87d1b3d23", "Coverage Profile Along Genes (High).png:md5,bbf0531018e7fccfc1dfdd1c05715518", "Coverage Profile Along Genes (Low).png:md5,3c147d9c831d4be98615a22a72fad05d", "Coverage Profile Along Genes (Total).png:md5,5a8a6db3a8d19a2dcb8f715b11e67c50", - "Junction Analysis.png:md5,f7597b8d428d092394ee6aab9731c4ef", - "Reads Genomic Origin.png:md5,e19e85335cf6f64495f4691f15cf39d8", "Transcript coverage histogram.png:md5,488440d7b6d73bcd4567316712e281fe", "coverage_profile_along_genes_(high).txt:md5,9f1e29a4d6eec52e8796b080daaedca3", "coverage_profile_along_genes_(low).txt:md5,353f42a84ff34167646fc83909eac2ff", "coverage_profile_along_genes_(total).txt:md5,353f42a84ff34167646fc83909eac2ff", - "rnaseq_qc_results.txt:md5,9c6543bf977cea9624aab0d2c0eb2640", "Coverage Profile Along Genes (High).png:md5,5a5d99cc7a1dba3762d67f4aa4adad58", "Coverage Profile Along 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Origin.png:md5,c99bbcf2882d7ab7a0093157faa69c72", "Transcript coverage histogram.png:md5,17404146ad5e0a9bce97ce622e00975e", "coverage_profile_along_genes_(high).txt:md5,8bf366c7dbc6170035ee64a057c581f1", "coverage_profile_along_genes_(low).txt:md5,a9102de3ff9679d1f7a86afa85997211", "coverage_profile_along_genes_(total).txt:md5,a9102de3ff9679d1f7a86afa85997211", - "rnaseq_qc_results.txt:md5,6bb8c2b18eb67b015bba7d92944cd687", "Coverage Profile Along Genes (High).png:md5,40edd79c21f3e8d8bbac384156c472d6", "Coverage Profile Along Genes (Low).png:md5,935c0372259a953a4c99569e9b236ae5", "Coverage Profile Along Genes (Total).png:md5,34f7a4307be1ea674b7b98eee564d96b", - "Junction Analysis.png:md5,147d7341869d7446ae0ad4dd1e3de700", - "Reads Genomic Origin.png:md5,93e1f3e32fa60a4dddc4ca696e1347f0", "Transcript coverage histogram.png:md5,e2abf8a9c62fef57f0be1ca0e01e502d", "coverage_profile_along_genes_(high).txt:md5,3f13eb908d6e97e6831306e9527cc2e3", "coverage_profile_along_genes_(low).txt:md5,24df553662d0cedaa74cf06a8fead40b", "coverage_profile_along_genes_(total).txt:md5,24df553662d0cedaa74cf06a8fead40b", - "rnaseq_qc_results.txt:md5,401d4141bd4d884b35faa4cb497311f7", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", - "qualimapReport.html" + "rnaseq_qc_results.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-22T17:43:26.686713" + "timestamp": "2024-08-26T14:18:38.410297" } } \ No newline at end of file diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 46c65ae09..0ec4de58a 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -226,12 +226,11 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_genome_result.names.txt"), file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annot.nameation_junctions_plot_Events.txt"), + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 2c6a78ff4..ba3b8e253 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -1,61 +1,16 @@ { "hisat2/rseqc": { "content": [ - "RAP1_IAA_30M_REP1.bam_stat.txt:md5,b38becac2242c9e565453a3147a3679e", - "RAP1_UNINDUCED_REP1.bam_stat.txt:md5,ae7a5e0ec19906b5f9e2fdb397ad14f3", - "RAP1_UNINDUCED_REP2.bam_stat.txt:md5,494fd84c2550aab95335092b9a12b582", - "WT_REP1.bam_stat.txt:md5,ae49a89df9a95984e0dcbde12b4f6c95", - "WT_REP2.bam_stat.txt:md5,3dc7a3e286e4c244b08df72010060696", "RAP1_IAA_30M_REP1.infer_experiment.txt:md5,1d4348685fa61819ff8076213d0873b3", "RAP1_UNINDUCED_REP1.infer_experiment.txt:md5,3ee0f64e82f0b1ac16b5f3e2b30b024c", "RAP1_UNINDUCED_REP2.infer_experiment.txt:md5,3d17628d178e5a3cc9dc03f32614bff7", "WT_REP1.infer_experiment.txt:md5,13e3c748f5b968455a39eb9fefd87053", "WT_REP2.infer_experiment.txt:md5,230910b354a5531d1c4bf711ccd6e493", - "RAP1_IAA_30M_REP1.junction.Interact.bed:md5,8b81a9250f08972f06f88bcfab43421f", - "RAP1_IAA_30M_REP1.junction.bed:md5,173eae77a0cd99001ff229c8bb839f6e", - "RAP1_UNINDUCED_REP1.junction.Interact.bed:md5,bed2f59ec92d15b5f90f1c2a14787d64", - "RAP1_UNINDUCED_REP1.junction.bed:md5,52a8150e3e4605f94519072fee16449b", - "RAP1_UNINDUCED_REP2.junction.Interact.bed:md5,928e134ad0621398ec59b3248f4bb08c", - "RAP1_UNINDUCED_REP2.junction.bed:md5,de5f7324e1e1958713b7460c9881e42e", - "WT_REP1.junction.Interact.bed:md5,ecd57f03d6a5c582c4c6c7ae13c05144", - "WT_REP1.junction.bed:md5,f5a188b82b4b993abf101b046043852c", - "WT_REP2.junction.Interact.bed:md5,a045b8e3f5b7c680272e0d415621fb3d", - "WT_REP2.junction.bed:md5,3d32038159734b9f1c9d366a090127d4", - "RAP1_IAA_30M_REP1.junction_annotation.log:md5,c06db08a16732003984ce0b7f7bf1fe8", - "RAP1_UNINDUCED_REP1.junction_annotation.log:md5,619a128b608946650338ef4eb1261dff", - "RAP1_UNINDUCED_REP2.junction_annotation.log:md5,f9a772dc8395f9266c81d666a56dc0ab", - "WT_REP1.junction_annotation.log:md5,934d6b1d55cb31cbfe183c7f838dc580", - "WT_REP2.junction_annotation.log:md5,02bf2e27dfd72fb89f3689c955dc57ed", - "RAP1_IAA_30M_REP1.junction_plot.r:md5,7d0e8b2937187d6e527ed70027f7b772", - "RAP1_UNINDUCED_REP1.junction_plot.r:md5,fa47ada2b36809228d1b50244e139733", - "RAP1_UNINDUCED_REP2.junction_plot.r:md5,5a9cdf301449dff95c5d5e708e687116", - "WT_REP1.junction_plot.r:md5,4b59b01d12839dcbce41f317e4c08a01", - "WT_REP2.junction_plot.r:md5,5f0daab3e17d4ae765042c6abaa6cff0", - "RAP1_IAA_30M_REP1.junction.xls:md5,98bf3cdbc11ecedc381be4b7ca7554f5", - "RAP1_UNINDUCED_REP1.junction.xls:md5,84f33de4ead9d9c778c1d74d7061f368", - "RAP1_UNINDUCED_REP2.junction.xls:md5,41169042d84d68782bbf41b4cdf5f7fe", - "WT_REP1.junction.xls:md5,dda86a7a53d4832067962356aa9c64b3", - "WT_REP2.junction.xls:md5,eb39b92002a7b2295d15318451e14d39", - "RAP1_IAA_30M_REP1.read_distribution.txt:md5,69f3731ebe31540eb34be1b581c88bdb", - "RAP1_UNINDUCED_REP1.read_distribution.txt:md5,8324ffb159a4e40555e6d088d7aa6e7f", - "RAP1_UNINDUCED_REP2.read_distribution.txt:md5,a658f427236d094aef6e65ea512a2642", - "WT_REP1.read_distribution.txt:md5,4202e7e0b800e897e76a5ce8bdd804d1", - "WT_REP2.read_distribution.txt:md5,b16004cf92f131094bc87c1aa3a9bd73", - "RAP1_IAA_30M_REP1.DupRate_plot.r:md5,449cc929b5c0afb6fe0d3c42aba022b1", - "RAP1_UNINDUCED_REP1.DupRate_plot.r:md5,9c733115d61e98bfd05bc4c6b010abdc", - "RAP1_UNINDUCED_REP2.DupRate_plot.r:md5,bd3a2f3806ff7d8a4f3a4d8f44ed8d2c", - "WT_REP1.DupRate_plot.r:md5,c0babc40356d96763f8f09a0c0ecf1b7", - "WT_REP2.DupRate_plot.r:md5,d38e55e5f22b2287a8ec2161df9351d7", - "RAP1_IAA_30M_REP1.pos.DupRate.xls:md5,0054db74dc0b03e0d322b41c1c89bf9a", - "RAP1_IAA_30M_REP1.seq.DupRate.xls:md5,55415fffae3175eb1d36e27c747460ef", - "RAP1_UNINDUCED_REP1.pos.DupRate.xls:md5,828df788550bb2cfd139bfb1bf5855a1", - "RAP1_UNINDUCED_REP1.seq.DupRate.xls:md5,dd22981ce08bdff7df4e35e5e10c3e27", - "RAP1_UNINDUCED_REP2.pos.DupRate.xls:md5,366805c99a2dfa508caf0b2728cae56b", - "RAP1_UNINDUCED_REP2.seq.DupRate.xls:md5,dd7b1c9fc2be67beb0bab769666e9a9d", - "WT_REP1.pos.DupRate.xls:md5,925c9a6b036fb3c19d7881700c544ed3", - "WT_REP1.seq.DupRate.xls:md5,68ca73f1471e38d38eb87f9f9a763a97", - "WT_REP2.pos.DupRate.xls:md5,18af139e2465d911039c825a83c547c4", - "WT_REP2.seq.DupRate.xls:md5,4174d14ca585c2109316b48645e479dc", + "RAP1_IAA_30M_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP1.bam_stat.txt", + "RAP1_UNINDUCED_REP2.bam_stat.txt", + "WT_REP1.bam_stat.txt", + "WT_REP2.bam_stat.txt", "RAP1_IAA_30M_REP1.inner_distance_plot.pdf", "WT_REP1.inner_distance_plot.pdf", "WT_REP2.inner_distance_plot.pdf", @@ -71,6 +26,21 @@ "WT_REP2.inner_distance.txt", "WT_REP2.inner_distance_freq.txt", "WT_REP2.inner_distance_mean.txt", + "RAP1_IAA_30M_REP1.junction.Interact.bed", + "RAP1_IAA_30M_REP1.junction.bed", + "RAP1_UNINDUCED_REP1.junction.Interact.bed", + "RAP1_UNINDUCED_REP1.junction.bed", + "RAP1_UNINDUCED_REP2.junction.Interact.bed", + "RAP1_UNINDUCED_REP2.junction.bed", + "WT_REP1.junction.Interact.bed", + "WT_REP1.junction.bed", + "WT_REP2.junction.Interact.bed", + "WT_REP2.junction.bed", + "RAP1_IAA_30M_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP1.junction_annotation.log", + "RAP1_UNINDUCED_REP2.junction_annotation.log", + "WT_REP1.junction_annotation.log", + "WT_REP2.junction_annotation.log", "RAP1_IAA_30M_REP1.splice_events.pdf", "RAP1_IAA_30M_REP1.splice_junction.pdf", "RAP1_UNINDUCED_REP1.splice_events.pdf", @@ -81,6 +51,16 @@ "WT_REP1.splice_junction.pdf", "WT_REP2.splice_events.pdf", "WT_REP2.splice_junction.pdf", + "RAP1_IAA_30M_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP1.junction_plot.r", + "RAP1_UNINDUCED_REP2.junction_plot.r", + "WT_REP1.junction_plot.r", + "WT_REP2.junction_plot.r", + "RAP1_IAA_30M_REP1.junction.xls", + "RAP1_UNINDUCED_REP1.junction.xls", + "RAP1_UNINDUCED_REP2.junction.xls", + "WT_REP1.junction.xls", + "WT_REP2.junction.xls", "RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf", "RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf", @@ -91,17 +71,37 @@ "RAP1_UNINDUCED_REP2.junctionSaturation_plot.r", "WT_REP1.junctionSaturation_plot.r", "WT_REP2.junctionSaturation_plot.r", + "RAP1_IAA_30M_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP1.read_distribution.txt", + "RAP1_UNINDUCED_REP2.read_distribution.txt", + "WT_REP1.read_distribution.txt", + "WT_REP2.read_distribution.txt", "RAP1_IAA_30M_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP1.DupRate_plot.pdf", "RAP1_UNINDUCED_REP2.DupRate_plot.pdf", "WT_REP1.DupRate_plot.pdf", - "WT_REP2.DupRate_plot.pdf" + "WT_REP2.DupRate_plot.pdf", + "RAP1_IAA_30M_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP1.DupRate_plot.r", + "RAP1_UNINDUCED_REP2.DupRate_plot.r", + "WT_REP1.DupRate_plot.r", + "WT_REP2.DupRate_plot.r", + "RAP1_IAA_30M_REP1.pos.DupRate.xls", + "RAP1_IAA_30M_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP1.pos.DupRate.xls", + "RAP1_UNINDUCED_REP1.seq.DupRate.xls", + "RAP1_UNINDUCED_REP2.pos.DupRate.xls", + "RAP1_UNINDUCED_REP2.seq.DupRate.xls", + "WT_REP1.pos.DupRate.xls", + "WT_REP1.seq.DupRate.xls", + "WT_REP2.pos.DupRate.xls", + "WT_REP2.seq.DupRate.xls" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:35:11.780439" + "timestamp": "2024-08-26T13:55:07.472724" }, "trimgalore": { "content": [ @@ -151,9 +151,6 @@ "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", "multiqc_picard_dups.txt:md5,71d5bafee1a4916951349018f387f7a0", - "multiqc_rseqc_bam_stat.txt:md5,b259b4e713d5c1b11f61e5f4c2f24660", - "multiqc_rseqc_junction_annotation.txt:md5,7576d6df2e66d72eebc0c2fb9f7fe56e", - "multiqc_rseqc_read_distribution.txt:md5,2254de1c5e6e726f085cb944e7a56442", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", "picard_deduplication.txt:md5,b54a144d4f23ade2221d7ca1af1997f4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -161,15 +158,9 @@ "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,f3b9bb1902af4c7b5e04c0830ded2c02", "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", - "qualimap_genomic_origin.txt:md5,dd514d2a42da9c4dd1ad4780aa4ac37e", "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", - "qualimap_rnaseq_genome_results.txt:md5,44d4f08e147731faf8bcc6ace52f00f2", - "rseqc_bam_stat.txt:md5,edfcffb5a74460da3870bec5522b2a3b", "rseqc_infer_experiment_plot.txt:md5,0556a013129be7d78fac4345fddbe8c5", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,db75ad02153035dea3ffaf58aa68894e", "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,d233f89c3c69a0dfc2e66d4d5b8c7ea1", - "rseqc_read_distribution_plot.txt:md5,243e8358c7cb5a13d99f715c70c624cb", - "rseqc_read_dups_plot.txt:md5,ed6a2aef667b65f49129c2af874fdbb5", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", @@ -191,7 +182,10 @@ "multiqc_hisat2_deseq2_clustering-plot_3.txt", "multiqc_hisat2_deseq2_clustering-plot_4.txt", "multiqc_hisat2_deseq2_pca-plot.txt", + "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", + "multiqc_rseqc_junction_annotation.txt", + "multiqc_rseqc_read_distribution.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -203,14 +197,19 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "qualimap_genomic_origin.txt", + "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt:md5,db75ad02153035dea3ffaf58aa68894e", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", @@ -220,7 +219,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T14:34:39.931494" + "timestamp": "2024-08-26T13:55:07.074305" }, "hisat2/picard_metrics": { "content": [ @@ -280,40 +279,40 @@ "content": [ "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e04029ba0b7c9a5007b1e21190416ab3", "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats:md5,85da324fea3cc89b59e98c35a088292d", "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,acdfa72b8fb5785abeddaabdab1ed8ca", "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_IAA_30M_REP1.sorted.bam.stats:md5,406e39a77140b36f00f8c66bf89e4cd4", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,b0b719dd29053aa37010082b6a0bb8d1", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats:md5,5a44fea09713c4eabb4c692ffa1c87cb", "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,0f82cf321c7ac21d11c29b7e8fd6893b", "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP1.sorted.bam.stats:md5,59269ee5c3c5cbe4d786e80d0ec3f82d", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,cb40075ffa2e6f66d8b4b5025fd62004", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats:md5,9c3328a52ad945726373add1acb544ea", "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,92d7610422de90da2e76f99461721b7f", "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "RAP1_UNINDUCED_REP2.sorted.bam.stats:md5,e513153ebdbb35255deb119e6d00899e", "WT_REP1.markdup.sorted.bam.flagstat:md5,cb3229294e384dba57b00ddab95e5cc9", "WT_REP1.markdup.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP1.markdup.sorted.bam.stats:md5,27296cfcca78a743c925a01598e479c4", "WT_REP1.sorted.bam.flagstat:md5,c55ed3c6ea5f4134036fa8a09c20a1ee", "WT_REP1.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP1.sorted.bam.stats:md5,8d99f380f036d5ebf93a62380888925e", "WT_REP2.markdup.sorted.bam.flagstat:md5,a0702469e2d220391604e1b72100cad1", "WT_REP2.markdup.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", - "WT_REP2.markdup.sorted.bam.stats:md5,f5cff907e667269f2667b173ae80fd0c", "WT_REP2.sorted.bam.flagstat:md5,b33836e522593ca0aed7c3b10973d5ed", "WT_REP2.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", - "WT_REP2.sorted.bam.stats:md5,e75ecf8f4c61acd5f5aa4fe48f753658" + "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:35:11.822891" + "timestamp": "2024-08-26T13:55:07.609425" }, "salmon/deseq2_qc": { "content": [ @@ -405,15 +404,9 @@ "picard_deduplication-pct.png:md5,dbced4008901ab031eda6d0d96ca038b", "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", - "qualimap_genomic_origin-cnt.png:md5,328eb53732bc789d4c9d0aedfc4bcdba", - "qualimap_genomic_origin-pct.png:md5,c5ac55b618d394325f8b0a02463d7ec5", "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", - "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,ac58787f8a0c8fadb4622482cf37f6ae", - "rseqc_junction_annotation_junctions_plot_Events-pct.png:md5,bff95e7ddaefdd86188ddb9751e0225f", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,4b91da0c996a436fe52a5b5ce4dee0bf", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,7b304888b33bce8e4c66475711a0a7d1", - "rseqc_read_distribution_plot-cnt.png:md5,07550051821e5b6b2dad0f99c60f2a3e", - "rseqc_read_distribution_plot-pct.png:md5,53cbf7df030a36f7a850580dc7cd6df0", "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -513,12 +506,18 @@ "hisat2_pe_plot-pct.png", "hisat2_se_plot-cnt.png", "hisat2_se_plot-pct.png", + "qualimap_genomic_origin-cnt.png", + "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png", + "rseqc_junction_annotation_junctions_plot_Events-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", @@ -603,7 +602,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T14:34:40.253371" + "timestamp": "2024-08-26T13:55:07.18703" }, "fastqc/raw": { "content": [ @@ -666,64 +665,64 @@ "Coverage Profile Along Genes (High).png:md5,99a8749fb819be0f1bde152e2246d964", "Coverage Profile Along Genes (Low).png:md5,31bed1d299f6e763c61a2866abc847c9", "Coverage Profile Along Genes (Total).png:md5,97d15c2ffd8163b800b1ca6378ae0ce9", - "Junction Analysis.png:md5,62f013dacfd7cd6c00781ed150c430f7", - "Reads Genomic Origin.png:md5,28cd03601bf408c39a97051919436db2", "Transcript coverage histogram.png:md5,a0cd920b7f67ee02deb4fd5ee5a5b0fc", "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", - "rnaseq_qc_results.txt:md5,5c981862809e2de3fdff9f9d20c43b38", "Coverage Profile Along Genes (High).png:md5,0c9e9983e2bb5688bca25d1697bcde9c", "Coverage Profile Along Genes (Low).png:md5,07df4715abe4e9c49265b7cecec79fe6", "Coverage Profile Along Genes (Total).png:md5,a4ed549db9b210e43955386957fdcd49", - "Junction Analysis.png:md5,e355c1e37f4ebf0d7968163c91edad9d", - "Reads Genomic Origin.png:md5,4bef06bc7da84b3fdfa7405a0fb90a0e", "Transcript coverage histogram.png:md5,1ee5a0ec7f0eec36dd51e312d303ea55", "coverage_profile_along_genes_(high).txt:md5,9ffadadb953cc9ea1b1c01ac92fcdf61", "coverage_profile_along_genes_(low).txt:md5,fb281c857a2c4e093b0d8e1f756abf81", "coverage_profile_along_genes_(total).txt:md5,fb281c857a2c4e093b0d8e1f756abf81", - "rnaseq_qc_results.txt:md5,ccdc9ab548f2838505cd1f3301b9651d", "Coverage Profile Along Genes (High).png:md5,9e530e83b3ab308ece285c115b7bde7d", "Coverage Profile Along Genes (Low).png:md5,b4181c86e9764bf7f543b24232ffea77", "Coverage Profile Along Genes (Total).png:md5,ec77f7b0919d8537f31ecf3a6dd245b0", - "Junction Analysis.png:md5,dba810f49cff8f3531dc6295330591c4", - "Reads Genomic Origin.png:md5,f8cccfa74bed0b7c1f473e5a3881ec40", "Transcript coverage histogram.png:md5,4017dc4254884805a327a6fd45e06562", "coverage_profile_along_genes_(high).txt:md5,a31cb4ba804080544072cd57fc1bdf1c", "coverage_profile_along_genes_(low).txt:md5,f744e295c3d034b1a86e1dde8bb18eff", "coverage_profile_along_genes_(total).txt:md5,f744e295c3d034b1a86e1dde8bb18eff", - "rnaseq_qc_results.txt:md5,200ad62a93ce4995af9ffe686c6cc1f4", "Coverage Profile Along Genes (High).png:md5,9e4a7aa85ae86a7ab5b1c949ed10d913", "Coverage Profile Along Genes (Low).png:md5,3f9d7d3842d827bb5a7a46a80e88e14b", "Coverage Profile Along Genes (Total).png:md5,44826c2d3263ff4aaedfa3b4d0c068db", - "Junction Analysis.png:md5,5cbb4dd431d6548f9a3a55b088e897f9", - "Reads Genomic Origin.png:md5,85d98f5475c6cc364b9add9dd1ed0b75", "Transcript coverage histogram.png:md5,51e934c908640c9dda94d3de8c4dd81f", "coverage_profile_along_genes_(high).txt:md5,be72a2c9023f6eb81bd5816af33abb65", "coverage_profile_along_genes_(low).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb", "coverage_profile_along_genes_(total).txt:md5,9fce120533ff57f8bc2a2f44f1b6decb", - "rnaseq_qc_results.txt:md5,2d7ef162c95fede85dca466bab3ba605", "Coverage Profile Along Genes (High).png:md5,f63458b8564de80c90c992926ea273ed", "Coverage Profile Along Genes (Low).png:md5,44f0dd7c647a2ce2c1f06e3920266e95", "Coverage Profile Along Genes (Total).png:md5,12780d9ad7b76dbdd39736099c45cf07", - "Junction Analysis.png:md5,501bbb899a0d79bf463bbbf1d70005c8", - "Reads Genomic Origin.png:md5,928f79166fb6adfccdc6eb4c54869156", "Transcript coverage histogram.png:md5,fcc848c9d318a28c7dff00cb2960e038", "coverage_profile_along_genes_(high).txt:md5,83d436e0ddb7435bb343db5e4dfb744a", "coverage_profile_along_genes_(low).txt:md5,58021e91f3595a0d6dc74abc41690638", "coverage_profile_along_genes_(total).txt:md5,58021e91f3595a0d6dc74abc41690638", - "rnaseq_qc_results.txt:md5,09508917659c8448598bf8b4f1a8f938", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", "qualimapReport.html", - "qualimapReport.html" + "rnaseq_qc_results.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-23T12:35:11.750007" + "timestamp": "2024-08-26T13:55:07.345475" }, "versions": { "content": [ From c5f26a943c76c5faa7c08f7fe55b510a1b3c649f Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 15:27:55 +0200 Subject: [PATCH 35/41] skip_trimming test and snapshots --- tests/skip_trimming.nf.test | 812 +++++++++++++++++++++++++- tests/skip_trimming.nf.test.snap | 943 +++++++++++++++++++++++++++++++ 2 files changed, 1754 insertions(+), 1 deletion(-) create mode 100644 tests/skip_trimming.nf.test.snap diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 28452df5c..e9915a43c 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -13,7 +13,817 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_salmon/bigwig/WT_REP2.reverse.bigWig").name + ).match("star_salmon/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_salmon/deseq2_qc/deseq2.sample.dists.txt").name + ).match("star_salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/star_salmon/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_salmon/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name + ).match("star_salmon/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt"), + // These files are unstable + file("${params.outdir}/star_salmon/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_salmon/featurecounts/WT_REP2.featureCounts.txt.summary").name + ).match("star_salmon/featurecounts") }, + { assert snapshot( + path("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP1.SJ.out.tab"), + path("${params.outdir}/star_salmon/log/WT_REP2.SJ.out.tab"), + // Logs are not stable + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_IAA_30M_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/RAP1_UNINDUCED_REP2.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP1.Log.progress.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.final.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.out").name, + file("${params.outdir}/star_salmon/log/WT_REP2.Log.progress.out").name + ).match("star_salmon/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_salmon/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_salmon/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_salmon/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_salmon/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + // HTML reports and these files are not stable + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/star_salmon/qualimap/WT_REP2/rnaseq_qc_results.txt").name + ).match("star_salmon/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/star_salmon/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/star_salmon/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name + ).match("star_salmon/rseqc") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name + ).match("star_salmon/salmon") }, + { assert snapshot( + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), + // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name + ).match("star_salmon/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_salmon/stringtie/WT_REP2.transcripts.gtf").name + ).match("star_salmon/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_salmon/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_salmon/markdup") }, + { assert snapshot( + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/star_salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/star_salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/star_salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/star_salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/star_salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/star_salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/star_salmon/WT_REP2/quant.sf").name + ).match("star_salmon/salmon_quant") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) } } } + +// STUB ARE CURRENTLY NOT POSSIBLE \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap new file mode 100644 index 000000000..9a4b86bcc --- /dev/null +++ b/tests/skip_trimming.nf.test.snap @@ -0,0 +1,943 @@ +{ + "star_salmon/log": { + "content": [ + "RAP1_IAA_30M_REP1.SJ.out.tab:md5,20c790387ef68e041bc4ffdcd032a22f", + "RAP1_UNINDUCED_REP1.SJ.out.tab:md5,ba2636236fa1d26aa72f7aff73bd41f8", + "RAP1_UNINDUCED_REP2.SJ.out.tab:md5,1c0458f66e4af56a56f4409c120434b3", + "WT_REP1.SJ.out.tab:md5,299a948b1aaf329152224ba573402a51", + "WT_REP2.SJ.out.tab:md5,073498a8fb5fb4da664c9129a6777c42", + "RAP1_IAA_30M_REP1.Log.final.out", + "RAP1_IAA_30M_REP1.Log.out", + "RAP1_IAA_30M_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP1.Log.final.out", + "RAP1_UNINDUCED_REP1.Log.out", + "RAP1_UNINDUCED_REP1.Log.progress.out", + "RAP1_UNINDUCED_REP2.Log.final.out", + "RAP1_UNINDUCED_REP2.Log.out", + "RAP1_UNINDUCED_REP2.Log.progress.out", + "WT_REP1.Log.final.out", + "WT_REP1.Log.out", + "WT_REP1.Log.progress.out", + "WT_REP2.Log.final.out", + "WT_REP2.Log.out", + "WT_REP2.Log.progress.out" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T15:27:29.632524" + }, + "star_salmon/salmon_quant": { + "content": [ + "ambig_info.tsv:md5,d1d3bd2a5617220b29a9063cb29f0578", + "expected_bias.gz:md5,3407f87245d0003e0ffbfdf6d8c04f20", + 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96b4369bf96ab47849345658a102beea6b3f29a1 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 17:06:35 +0200 Subject: [PATCH 36/41] update test and snapshots --- tests/default.nf.test | 6 +++--- tests/default.nf.test.snap | 10 +++++----- tests/featurecounts_group_type.nf.test | 8 ++++---- tests/featurecounts_group_type.nf.test.snap | 12 ++++++------ tests/hisat2.nf.test | 8 ++++---- tests/hisat2.nf.test.snap | 12 ++++++------ tests/min_mapped_reads.nf.test | 6 +++--- tests/min_mapped_reads.nf.test.snap | 10 +++++----- tests/remove_ribo_rna.nf.test | 6 +++--- tests/remove_ribo_rna.nf.test.snap | 10 +++++----- tests/skip_trimming.nf.test | 11 ++++++----- tests/skip_trimming.nf.test.snap | 10 +++++----- 12 files changed, 55 insertions(+), 54 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index ca3929641..3b81a3a6c 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -103,7 +103,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -146,6 +145,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -189,8 +189,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -291,6 +289,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 330a0bc6e..ba779ac75 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -325,8 +325,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,e7636c4fcd19e7b7bb1731ac7e60d7ea", "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -426,6 +424,8 @@ "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -519,7 +519,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:44:57.525336" + "timestamp": "2024-08-26T16:21:24.616733" }, "fastqc/raw": { "content": [ @@ -704,7 +704,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -746,6 +745,7 @@ "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -764,7 +764,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:44:57.429315" + "timestamp": "2024-08-26T16:21:24.483792" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 9ec8f1aa6..08dcda953 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -103,7 +103,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -146,6 +145,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -187,8 +187,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -285,8 +283,10 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png"), + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 6c136b14e..078ab9d3d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -132,7 +132,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,eeeea7f50278b3b335bef545784abbfa", "qualimap_rnaseq_cov_hist.txt:md5,51407e597076f3a7f98622213bea6bce", "rseqc_infer_experiment_plot.txt:md5,de5a0bad9cca763928e7c33375eb5218", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,454eb9917793890ee4837fce43e3a8dd", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -174,6 +173,7 @@ "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -192,7 +192,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:52:52.937207" + "timestamp": "2024-08-26T16:29:22.875142" }, "trimgalore": { "content": [ @@ -474,8 +474,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,a01190d3ad8e4b9cede321d56e633ec7", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,e7636c4fcd19e7b7bb1731ac7e60d7ea", "rseqc_read_dups_plot.png:md5,958513925fa5494bf499c989842d6928", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -571,8 +569,10 @@ "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", - "rseqc_junction_annotation_junctions_plot_Events-cnt.png:md5,1003e4b5012bbddc40badd9e2dfdda8e", + "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -664,7 +664,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T14:18:38.023639" + "timestamp": "2024-08-26T16:29:22.943986" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 0ec4de58a..484931d0b 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -187,7 +187,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -230,7 +229,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt"), + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -272,8 +272,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -381,6 +379,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index ba3b8e253..c3c508b2e 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -160,7 +160,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,ebcedec8e5c959414a4e89ccae3fc07e", "qualimap_rnaseq_cov_hist.txt:md5,b78ff616f267f9b061b3297b767e88fb", "rseqc_infer_experiment_plot.txt:md5,0556a013129be7d78fac4345fddbe8c5", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,d233f89c3c69a0dfc2e66d4d5b8c7ea1", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", @@ -202,7 +201,8 @@ "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt:md5,db75ad02153035dea3ffaf58aa68894e", + "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -219,7 +219,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:55:07.074305" + "timestamp": "2024-08-26T16:35:09.357006" }, "hisat2/picard_metrics": { "content": [ @@ -405,8 +405,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,4b91da0c996a436fe52a5b5ce4dee0bf", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,7b304888b33bce8e4c66475711a0a7d1", "rseqc_read_dups_plot.png:md5,fbb8a2268f0468be5a94c960bd2ebd2a", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -513,6 +511,8 @@ "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -602,7 +602,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:55:07.18703" + "timestamp": "2024-08-26T16:35:09.426445" }, "fastqc/raw": { "content": [ diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index 208425695..ce5a8b780 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -105,7 +105,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -148,6 +147,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -192,8 +192,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -293,6 +291,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 242c9522c..8d6d24c80 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -247,8 +247,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c", "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e", "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,b252097b89f67ded63380fb3c45ee2cb", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,85ff09e0c3ee207bdd72d69db7ec0461", "rseqc_read_dups_plot.png:md5,bdc7281c52b54a5784aa0d714f9c255e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -347,6 +345,8 @@ "qualimap_genomic_origin-pct.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_read_distribution_plot-cnt.png", "rseqc_read_distribution_plot-pct.png", "rseqc_inner_distance_plot_Counts.png", @@ -443,7 +443,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:36.880437" + "timestamp": "2024-08-26T16:42:10.506344" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -644,7 +644,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,dc8b4f9fddc08e06668f9ee87faac008", "qualimap_rnaseq_cov_hist.txt:md5,a409821701f60811027daef4e7f3ebee", "rseqc_infer_experiment_plot.txt:md5,749a802379ada3ec9d2083ecbe6aef7e", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,b4d76efb9fe0c30418b78dd6c61c42fa", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", @@ -686,6 +685,7 @@ "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -704,7 +704,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:36.810224" + "timestamp": "2024-08-26T16:42:10.446106" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index 4acb69a7e..f73f98286 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -104,7 +104,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -125,6 +124,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, @@ -192,8 +192,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -298,6 +296,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 0199ff877..9e1c4be55 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -294,8 +294,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598", "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00", "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,02a58fa6112699eb73a10bc62e8ff562", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,ccace8d19fd96e93939c9d446640dc37", "rseqc_read_dups_plot.png:md5,1a18ce4ca5f36722f1fdd579d7eb41e1", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -399,6 +397,8 @@ "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -494,7 +494,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:35.873754" + "timestamp": "2024-08-26T16:55:04.146511" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -710,7 +710,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,6ed32f112c679e73396350cbe5cb9459", "qualimap_rnaseq_cov_hist.txt:md5,a895b3af229f661da1edbc21ec72edaa", "rseqc_infer_experiment_plot.txt:md5,d8741451248f1a5a4ebe3230c1af9c95", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,f4aa74934a4c73c2c8a1b78866090419", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", @@ -730,6 +729,7 @@ "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_read_distribution_plot.txt", "rseqc_read_dups_plot.txt", "multiqc_rseqc_infer_experiment.txt", @@ -772,7 +772,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:35.782125" + "timestamp": "2024-08-26T16:55:04.076927" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index e9915a43c..23820fc94 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -70,7 +70,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_infer_experiment_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), @@ -112,6 +111,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, @@ -143,8 +143,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), @@ -225,6 +223,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, @@ -824,6 +824,7 @@ nextflow_pipeline { ) } } -} -// STUB ARE CURRENTLY NOT POSSIBLE \ No newline at end of file + // STUB ARE CURRENTLY NOT POSSIBLE + +} \ No newline at end of file diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 9a4b86bcc..2d36963fa 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -118,7 +118,6 @@ "qualimap_gene_coverage_profile_Normalised.txt:md5,209b0020fcd4c3c497e3abbd1f8cd593", "qualimap_rnaseq_cov_hist.txt:md5,3be7bc41531ce84b42092a742bfeb0ab", "rseqc_infer_experiment_plot.txt:md5,382397ae264336395e2a3b03af8d7023", - "rseqc_junction_annotation_junctions_plot_Junctions.txt:md5,426b963c80ceb1ec4849d03da27e0570", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525", @@ -159,6 +158,7 @@ "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", @@ -177,7 +177,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T15:27:28.25949" + "timestamp": "2024-08-26T17:04:58.433949" }, "star_salmon/rseqc": { "content": [ @@ -461,8 +461,6 @@ "qualimap_gene_coverage_profile_Counts.png:md5,8312f777db61509caa66d1f53a4b6b07", "qualimap_gene_coverage_profile_Normalised.png:md5,66acb12427130766801a8376f95ed88b", "rseqc_infer_experiment_plot.png:md5,c3108e35020ee93a77a62ea0167613b2", - "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png:md5,7f7ed45c326f7e597af2c59e5ec866b7", - "rseqc_junction_annotation_junctions_plot_Junctions-pct.png:md5,fecfef6063c049f440e1b9204f656502", "rseqc_read_dups_plot.png:md5,1e43ad78c4a87f7736b552ad71d25c16", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", @@ -542,6 +540,8 @@ "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", + "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", + "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", @@ -619,7 +619,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T15:27:28.389648" + "timestamp": "2024-08-26T17:04:58.556659" }, "star_salmon/picard_metrics": { "content": [ From 515f182383126d24b6c48ac0230786ab206e9964 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 17:39:48 +0200 Subject: [PATCH 37/41] fix linting + star_rsem tests and snapshots --- tests/skip_trimming.nf.test | 2 +- tests/star_rsem.nf.test | 899 ++++++++++++++++++++++++++++- tests/star_rsem.nf.test.snap | 1029 ++++++++++++++++++++++++++++++++++ 3 files changed, 1928 insertions(+), 2 deletions(-) create mode 100644 tests/star_rsem.nf.test.snap diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 23820fc94..912ebc13f 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -827,4 +827,4 @@ nextflow_pipeline { // STUB ARE CURRENTLY NOT POSSIBLE -} \ No newline at end of file +} diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 3a0b867a9..94f5d6fd9 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -13,7 +13,904 @@ nextflow_pipeline { } then { - assert workflow.success + assertAll( + { assert workflow.success }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/bbsplit/RAP1_IAA_30M_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/RAP1_UNINDUCED_REP2.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP1.stats.txt").name, + file("${params.outdir}/bbsplit/WT_REP2.stats.txt").name + ).match("bbsplit") }, + { assert snapshot( + path("${params.outdir}/custom/out/genome_gfp.fasta"), + path("${params.outdir}/custom/out/genome_gfp.gtf") + ).match("references") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw_2_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_1_fastqc.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw_2_fastqc.zip").name + ).match("fastqc/raw") }, + { assert snapshot( + // HTMLs and ZIPs are not stable + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_IAA_30M_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP1_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.html").name, + file("${params.outdir}/fastqc/trim/RAP1_UNINDUCED_REP2_trimmed_trimmed_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP1_trimmed_2_val_2_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_1_val_1_fastqc.zip").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.html").name, + file("${params.outdir}/fastqc/trim/WT_REP2_trimmed_2_val_2_fastqc.zip").name + ).match("fastqc/trim") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_assignment_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_multimapping_rates.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_infer_experiment_plot.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt"), + // These files are not stable + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_data.json").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_all.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_distribution_plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_read_dups_plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/salmon_plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_alignment_plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_summary_table.txt").name + ).match("multiqc_data") }, + { assert snapshot( + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-cnt.pdf"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-pct.pdf"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_multimapping_rates.pdf"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_multimapping_rates.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-cnt.svg"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-pct.svg"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_multimapping_rates.svg"), + // PDFs, SVGs, some PNGs and HTML reports are not stable + file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/picard_deduplication-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Percentages.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Events-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_annotation_junctions_plot_Junctions-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_All_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Known_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_junction_saturation_plot_Novel_Junctions.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/star_summary_table.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_summary_table.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/picard_deduplication-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Percentages.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Events-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_annotation_junctions_plot_Junctions-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_All_Junctions.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Known_Junctions.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_junction_saturation_plot_Novel_Junctions.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/star_summary_table.svg").name + ).match("multiqc_plots") }, + { assert snapshot( + path("${params.outdir}/salmon/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/salmon/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/salmon/deseq2_qc/deseq2.sample.dists.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/salmon/deseq2_qc/size_factors/deseq2.size_factors.RData").name + ).match("salmon/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_IAA_30M_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/cmd_info.json"), + path("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP1/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP1/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP1/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP1/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP1/lib_format_counts.json"), + path("${params.outdir}/salmon/WT_REP2/aux_info/ambig_info.tsv"), + path("${params.outdir}/salmon/WT_REP2/aux_info/expected_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias.gz"), + path("${params.outdir}/salmon/WT_REP2/aux_info/observed_bias_3p.gz"), + path("${params.outdir}/salmon/WT_REP2/cmd_info.json"), + path("${params.outdir}/salmon/WT_REP2/lib_format_counts.json"), + // These files are not stable + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_IAA_30M_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP1/quant.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/RAP1_UNINDUCED_REP2/quant.sf").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP1/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP1/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP1/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP1/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP1/quant.sf").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/fld.gz").name, + file("${params.outdir}/salmon/WT_REP2/aux_info/meta_info.json").name, + file("${params.outdir}/salmon/WT_REP2/libParams/flenDist.txt").name, + file("${params.outdir}/salmon/WT_REP2/logs/salmon_quant.log").name, + file("${params.outdir}/salmon/WT_REP2/quant.genes.sf").name, + file("${params.outdir}/salmon/WT_REP2/quant.sf").name + ).match("salmon_quant") }, + { assert snapshot( + path("${params.outdir}/salmon/tx2gene.tsv"), + // These files are not stable + file("${params.outdir}/salmon/salmon.merged.gene_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_length_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.gene_counts_scaled.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.gene_tpm.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.SummarizedExperiment.rds").name, + file("${params.outdir}/salmon/salmon.merged.transcript_counts.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_lengths.tsv").name, + file("${params.outdir}/salmon/salmon.merged.transcript_tpm.tsv").name + ).match("salmon") }, + { assert snapshot( + // These files are not stable + file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.forward.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/RAP1_IAA_30M_REP1.reverse.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.forward.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP1.reverse.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.forward.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/RAP1_UNINDUCED_REP2.reverse.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/WT_REP1.forward.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/WT_REP1.reverse.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/WT_REP2.forward.bigWig").name, + file("${params.outdir}/star_rsem/bigwig/WT_REP2.reverse.bigWig").name + ).match("star_rsem/bigwig") }, + { assert snapshot( + path("${params.outdir}/star_rsem/deseq2_qc/R_sessionInfo.log"), + // These files are not stable + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_IAA_30M_REP1.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP1.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/RAP1_UNINDUCED_REP2.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP1.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/WT_REP2.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/size_factors/deseq2.size_factors.RData").name, + file("${params.outdir}/star_rsem/deseq2_qc/deseq2.dds.RData").name, + file("${params.outdir}/star_rsem/deseq2_qc/deseq2.pca.vals.txt").name, + file("${params.outdir}/star_rsem/deseq2_qc/deseq2.plots.pdf").name, + file("${params.outdir}/star_rsem/deseq2_qc/deseq2.sample.dists.txt").name + ).match("star_rsem/deseq2_qc") }, + { assert snapshot( + path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_IAA_30M_REP1_dupMatrix.txt"), + path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP1_dupMatrix.txt"), + path("${params.outdir}/star_rsem/dupradar/gene_data/RAP1_UNINDUCED_REP2_dupMatrix.txt"), + path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP1_dupMatrix.txt"), + path("${params.outdir}/star_rsem/dupradar/gene_data/WT_REP2_dupMatrix.txt"), + path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_IAA_30M_REP1_intercept_slope.txt"), + path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP1_intercept_slope.txt"), + path("${params.outdir}/star_rsem/dupradar/intercepts_slope/RAP1_UNINDUCED_REP2_intercept_slope.txt"), + path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP1_intercept_slope.txt"), + path("${params.outdir}/star_rsem/dupradar/intercepts_slope/WT_REP2_intercept_slope.txt"), + // PDFs are not stable + file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_rsem/dupradar/box_plot/RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP1_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_rsem/dupradar/box_plot/WT_REP2_duprateExpBoxplot.pdf").name, + file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_IAA_30M_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_rsem/dupradar/histogram/RAP1_UNINDUCED_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP1_expressionHist.pdf").name, + file("${params.outdir}/star_rsem/dupradar/histogram/WT_REP2_expressionHist.pdf").name, + file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_IAA_30M_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_rsem/dupradar/scatter_plot/RAP1_UNINDUCED_REP2_duprateExpDens.pdf").name, + file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP1_duprateExpDens.pdf").name, + file("${params.outdir}/star_rsem/dupradar/scatter_plot/WT_REP2_duprateExpDens.pdf").name + ).match("star_rsem/dupradar") }, + { assert snapshot( + path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP1.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP2.biotype_counts_rrna_mqc.tsv"), + path("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt"), + // These files are unstable + file("${params.outdir}/star_rsem/featurecounts/RAP1_IAA_30M_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_rsem/featurecounts/RAP1_UNINDUCED_REP2.featureCounts.txt.summary").name, + file("${params.outdir}/star_rsem/featurecounts/WT_REP1.featureCounts.txt.summary").name, + file("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt.summary").name + ).match("star_rsem/featurecounts") }, + { assert snapshot( + path("${params.outdir}/star_rsem/log/RAP1_IAA_30M_REP1.log"), + path("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP1.log"), + path("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP2.log"), + path("${params.outdir}/star_rsem/log/WT_REP1.log"), + path("${params.outdir}/star_rsem/log/WT_REP2.log") + ).match("star_rsem/log") }, + { assert snapshot( + // Metrics are not stable + file("${params.outdir}/star_rsem/picard_metrics/RAP1_IAA_30M_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_rsem/picard_metrics/RAP1_UNINDUCED_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_rsem/picard_metrics/WT_REP1.markdup.sorted.MarkDuplicates.metrics.txt").name, + file("${params.outdir}/star_rsem/picard_metrics/WT_REP2.markdup.sorted.MarkDuplicates.metrics.txt").name + ).match("star_rsem/picard_metrics") }, + { assert snapshot( + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP1/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (High).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Low).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Coverage Profile Along Genes (Total).png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Transcript coverage histogram.png"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(high).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(low).txt"), + path("${params.outdir}/star_rsem/qualimap/WT_REP2/raw_data_qualimapReport/coverage_profile_along_genes_(total).txt"), + // HTML reports and these files are not stable + file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/qualimapReport.html").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_IAA_30M_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/qualimapReport.html").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/qualimapReport.html").name, + file("${params.outdir}/star_rsem/qualimap/RAP1_UNINDUCED_REP2/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP1/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP1/qualimapReport.html").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP1/rnaseq_qc_results.txt").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Junction Analysis.png").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP2/images_qualimapReport/Reads Genomic Origin.png").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP2/qualimapReport.html").name, + file("${params.outdir}/star_rsem/qualimap/WT_REP2/rnaseq_qc_results.txt").name + ).match("star_rsem/qualimap") }, + { assert snapshot( + path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.genes.results"), + path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.isoforms.results"), + path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.cnt"), + path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.model"), + path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.theta"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.genes.results"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.isoforms.results"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.cnt"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.model"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.theta"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.genes.results"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.isoforms.results"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.cnt"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.model"), + path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.theta"), + path("${params.outdir}/star_rsem/WT_REP1.genes.results"), + path("${params.outdir}/star_rsem/WT_REP1.isoforms.results"), + path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.cnt"), + path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.model"), + path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.theta"), + path("${params.outdir}/star_rsem/WT_REP2.genes.results"), + path("${params.outdir}/star_rsem/WT_REP2.isoforms.results"), + path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.cnt"), + path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.model"), + path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.theta"), + path("${params.outdir}/star_rsem/rsem.merged.gene_counts.tsv"), + path("${params.outdir}/star_rsem/rsem.merged.gene_tpm.tsv"), + path("${params.outdir}/star_rsem/rsem.merged.transcript_counts.tsv"), + path("${params.outdir}/star_rsem/rsem.merged.transcript_tpm.tsv") + ).match("star_rsem/rsem") }, + { assert snapshot( + path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), + path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP1.infer_experiment.txt"), + path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_UNINDUCED_REP2.infer_experiment.txt"), + path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP1.infer_experiment.txt"), + path("${params.outdir}/star_rsem/rseqc/infer_experiment/WT_REP2.infer_experiment.txt"), + // PDFs, R scripts and all these files are not stable + file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_IAA_30M_REP1.bam_stat.txt").name, + file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP1.bam_stat.txt").name, + file("${params.outdir}/star_rsem/rseqc/bam_stat/RAP1_UNINDUCED_REP2.bam_stat.txt").name, + file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP1.bam_stat.txt").name, + file("${params.outdir}/star_rsem/rseqc/bam_stat/WT_REP2.bam_stat.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/RAP1_IAA_30M_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP1.inner_distance_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/pdf/WT_REP2.inner_distance_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/RAP1_IAA_30M_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP1.inner_distance_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/rscript/WT_REP2.inner_distance_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/RAP1_IAA_30M_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_freq.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP1.inner_distance_mean.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_freq.txt").name, + file("${params.outdir}/star_rsem/rseqc/inner_distance/txt/WT_REP2.inner_distance_mean.txt").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_IAA_30M_REP1.junction.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP1.junction.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/RAP1_UNINDUCED_REP2.junction.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.Interact.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP1.junction.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.Interact.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/bed/WT_REP2.junction.bed").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_IAA_30M_REP1.junction_annotation.log").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP1.junction_annotation.log").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/RAP1_UNINDUCED_REP2.junction_annotation.log").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP1.junction_annotation.log").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/log/WT_REP2.junction_annotation.log").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_events.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_IAA_30M_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_events.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_events.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/RAP1_UNINDUCED_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_events.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP1.splice_junction.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_events.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/pdf/WT_REP2.splice_junction.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_IAA_30M_REP1.junction_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP1.junction_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/RAP1_UNINDUCED_REP2.junction_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP1.junction_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/rscript/WT_REP2.junction_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_IAA_30M_REP1.junction.xls").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP1.junction.xls").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/RAP1_UNINDUCED_REP2.junction.xls").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP1.junction.xls").name, + file("${params.outdir}/star_rsem/rseqc/junction_annotation/xls/WT_REP2.junction.xls").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_IAA_30M_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/RAP1_UNINDUCED_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP1.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/pdf/WT_REP2.junctionSaturation_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_IAA_30M_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/RAP1_UNINDUCED_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP1.junctionSaturation_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/junction_saturation/rscript/WT_REP2.junctionSaturation_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_IAA_30M_REP1.read_distribution.txt").name, + file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP1.read_distribution.txt").name, + file("${params.outdir}/star_rsem/rseqc/read_distribution/RAP1_UNINDUCED_REP2.read_distribution.txt").name, + file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP1.read_distribution.txt").name, + file("${params.outdir}/star_rsem/rseqc/read_distribution/WT_REP2.read_distribution.txt").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_IAA_30M_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/RAP1_UNINDUCED_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP1.DupRate_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/pdf/WT_REP2.DupRate_plot.pdf").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_IAA_30M_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/RAP1_UNINDUCED_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP1.DupRate_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/rscript/WT_REP2.DupRate_plot.r").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_IAA_30M_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.pos.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls").name, + file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name + ).match("star_rsem/rseqc") }, + { assert snapshot( + path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.flagstat"), + path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.idxstats"), + // These files are not stable + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.stats").name + ).match("star_rsem/samtools_stats") }, + { assert snapshot( + path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/i_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/e_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/i_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/e_data.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i2t.ctab"), + path("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/i_data.ctab"), + // These files are not stable + file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.coverage.gtf").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_IAA_30M_REP1.transcripts.gtf").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.coverage.gtf").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP1.transcripts.gtf").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.coverage.gtf").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_rsem/stringtie/RAP1_UNINDUCED_REP2.transcripts.gtf").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP1.ballgown/t_data.ctab").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP1.coverage.gtf").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP1.gene.abundance.txt").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP1.transcripts.gtf").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP2.ballgown/t_data.ctab").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP2.coverage.gtf").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP2.gene.abundance.txt").name, + file("${params.outdir}/star_rsem/stringtie/WT_REP2.transcripts.gtf").name + ).match("star_rsem/stringtie") }, + { assert snapshot( + file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam").name, + file("${params.outdir}/star_rsem/WT_REP1.markdup.sorted.bam.bai").name, + file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam").name, + file("${params.outdir}/star_rsem/WT_REP2.markdup.sorted.bam.bai").name + ).match("star_rsem/markdup") }, + { assert snapshot( + // These reports are not stable + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match("trimgalore") }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml") + ).match("versions") } + ) + } + } + + test("Params: --aligner star_rsem - stub") { + + options "-stub" + + when { + params { + outdir = "$outputDir" + aligner = 'star_rsem' + } + } + + then { + assertAll( + { assert workflow.success }, + { assert snapshot( + UTILS.removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), + file("${params.outdir}/custom/out/genome_transcriptome.fasta").name, + file("${params.outdir}/custom/out/genome_transcriptome.gtf").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_IAA_30M_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/RAP1_UNINDUCED_REP2_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP1_raw.zip").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.html").name, + file("${params.outdir}/fastqc/raw/WT_REP2_raw.zip").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_IAA_30M_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP1_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/RAP1_UNINDUCED_REP2_trimmed.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP1_trimmed_2.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_1.fastq.gz_trimming_report.txt").name, + file("${params.outdir}/trimgalore/WT_REP2_trimmed_2.fastq.gz_trimming_report.txt").name + ).match() } + ) } } } diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap new file mode 100644 index 000000000..beefc9b53 --- /dev/null +++ b/tests/star_rsem.nf.test.snap @@ -0,0 +1,1029 @@ +{ + "star_rsem/bigwig": { + "content": [ + "RAP1_IAA_30M_REP1.forward.bigWig", + "RAP1_IAA_30M_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP1.forward.bigWig", + "RAP1_UNINDUCED_REP1.reverse.bigWig", + "RAP1_UNINDUCED_REP2.forward.bigWig", + "RAP1_UNINDUCED_REP2.reverse.bigWig", + "WT_REP1.forward.bigWig", + "WT_REP1.reverse.bigWig", + "WT_REP2.forward.bigWig", + "WT_REP2.reverse.bigWig" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T17:25:04.845767" + }, + "star_rsem/dupradar": { + "content": [ + "RAP1_IAA_30M_REP1_dupMatrix.txt:md5,8da31020df3c5b25167345609c6d08c5", + "RAP1_UNINDUCED_REP1_dupMatrix.txt:md5,3f269a6b2e9c8eaab66582e31d208dfc", + "RAP1_UNINDUCED_REP2_dupMatrix.txt:md5,7d96d6ddf1d12d43837b105865aeaafa", + "WT_REP1_dupMatrix.txt:md5,802dd0de10d9118943869239f8659c78", + "WT_REP2_dupMatrix.txt:md5,e97a3c8d2e606d7d4b40cd33eb0b96c4", + "RAP1_IAA_30M_REP1_intercept_slope.txt:md5,d280fe126a5e82d24121d8662fd5a161", + "RAP1_UNINDUCED_REP1_intercept_slope.txt:md5,a498640b0f9e710311ebc3eb67cedbd0", + "RAP1_UNINDUCED_REP2_intercept_slope.txt:md5,a1c5346e3bad40546c793b8914a22e7e", + "WT_REP1_intercept_slope.txt:md5,9c2e2b7890427e79c97e65827102d965", + "WT_REP2_intercept_slope.txt:md5,db7a36459f2036de6657e74d2c98a47c", + "RAP1_IAA_30M_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP1_duprateExpBoxplot.pdf", + "RAP1_UNINDUCED_REP2_duprateExpBoxplot.pdf", + "WT_REP1_duprateExpBoxplot.pdf", + "WT_REP2_duprateExpBoxplot.pdf", + "RAP1_IAA_30M_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP1_expressionHist.pdf", + "RAP1_UNINDUCED_REP2_expressionHist.pdf", + "WT_REP1_expressionHist.pdf", + "WT_REP2_expressionHist.pdf", + "RAP1_IAA_30M_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP1_duprateExpDens.pdf", + "RAP1_UNINDUCED_REP2_duprateExpDens.pdf", + "WT_REP1_duprateExpDens.pdf", + "WT_REP2_duprateExpDens.pdf" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T17:25:05.410414" + }, + "multiqc_data": { + "content": [ + "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_trimmed_sequences_plot_3_Counts.txt:md5,13dfa866fd91dbb072689efe9aa83b1f", + "cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt:md5,07145dd8dd3db654859b18eb0389046c", + "fastqc-status-check-heatmap-1.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_overrepresented_sequences_plot-1.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_per_base_n_content_plot-1.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_per_base_sequence_quality_plot-1.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_per_sequence_gc_content_plot-1_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_per_sequence_gc_content_plot-1_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_per_sequence_quality_scores_plot-1.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_sequence_counts_plot-1.txt:md5,3861354bbedfbde7ca36a72994f9425c", + "fastqc_sequence_counts_plot.txt:md5,d385a3e2c2573a0902c66e8c93876d3c", + "fastqc_sequence_duplication_levels_plot-1.txt:md5,c73407d55fc532e864fa1dc8dbc12874", + "fastqc_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "multiqc_citations.txt:md5,5a68f7972ea275b21b12acdf43447dfb", + "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", + "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", + "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", + "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", + "multiqc_picard_dups.txt:md5,0e258d3ce451fa5233c81a631c807636", + "multiqc_rsem.txt:md5,426cfb38a96c0d7111336be3164171fb", + "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", + "picard_deduplication.txt:md5,b6e23251b2007c0759c347aaa31d2a76", + "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", + "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", + "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", + "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", + "rsem_assignment_plot.txt:md5,136b1ca144da9a1b304ff3471ff44390", + "rsem_multimapping_rates.txt:md5,5d91bb56472834622e81e7919f746250", + "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", + 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"qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt", + "Junction Analysis.png", + "Reads Genomic Origin.png", + "qualimapReport.html", + "rnaseq_qc_results.txt" + ], + "meta": { + "nf-test": "0.9.0", + "nextflow": "24.04.4" + }, + "timestamp": "2024-08-26T17:25:05.907994" + } +} \ No newline at end of file From 14c5118ec5b9b8b614dc205e98d4cc3d4a0c4495 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 17:40:48 +0200 Subject: [PATCH 38/41] update CHANGELOG --- CHANGELOG.md | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 81f74ba7a..11241e5b2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -115,7 +115,11 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests - [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround +<<<<<<< Updated upstream - [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map +======= +- [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests +>>>>>>> Stashed changes - [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module ### Parameters From 1ad7865309839300cbaa03ba2a2e932e7b817a9c Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 17:42:32 +0200 Subject: [PATCH 39/41] fix merge conflicts --- CHANGELOG.md | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 11241e5b2..147e7d42c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -115,11 +115,8 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements - [PR #1357](https://github.com/nf-core/rnaseq/pull/1357) - Fix anchor issue in multiqc - [PR #1358](https://github.com/nf-core/rnaseq/pull/1358) - Update test profiles to restore a static URI for megatests - [PR #1359](https://github.com/nf-core/rnaseq/pull/1359) - Update MultiQC and revert unnecessary workaround -<<<<<<< Updated upstream -- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map -======= - [PR #1360](https://github.com/nf-core/rnaseq/pull/1360) - More complete snapshots for pipeline level tests ->>>>>>> Stashed changes +- [PR #1361](https://github.com/nf-core/rnaseq/pull/1361) - Animate subway map - [PR #1362](https://github.com/nf-core/rnaseq/pull/1362) - Move multiqc module prefix for nf-test to module ### Parameters From 056ce81f2720a1aad7a759469346d1900520ae63 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 18:31:42 +0200 Subject: [PATCH 40/41] update tests --- tests/default.nf.test | 54 +++++------ tests/featurecounts_group_type.nf.test | 54 +++++------ tests/hisat2.nf.test | 62 ++++++------- tests/min_mapped_reads.nf.test | 56 ++++++------ tests/remove_ribo_rna.nf.test | 70 +++++++------- tests/skip_qc.nf.test | 54 +++++------ tests/skip_trimming.nf.test | 54 +++++------ tests/star_rsem.nf.test | 121 +++++++++++++------------ 8 files changed, 264 insertions(+), 261 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 3b81a3a6c..069bb846f 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -93,9 +93,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), @@ -106,7 +104,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -116,6 +113,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -138,6 +136,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, @@ -157,6 +156,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, @@ -184,8 +184,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -196,8 +194,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -282,6 +278,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, @@ -302,6 +300,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, @@ -754,36 +754,36 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/featurecounts_group_type.nf.test b/tests/featurecounts_group_type.nf.test index 08dcda953..16794293b 100644 --- a/tests/featurecounts_group_type.nf.test +++ b/tests/featurecounts_group_type.nf.test @@ -93,9 +93,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), @@ -106,7 +104,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -116,6 +113,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -138,6 +136,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, @@ -157,6 +156,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, @@ -182,8 +182,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -194,8 +192,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -278,6 +274,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, @@ -298,6 +296,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, @@ -725,36 +725,36 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 484931d0b..67ae1187e 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -177,9 +177,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_histogram_2.txt"), @@ -190,7 +188,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -209,6 +206,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_hisat2_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -224,6 +222,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/multiqc_sources.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/rseqc_inner_distance.txt").name, @@ -242,6 +241,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name, ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), @@ -267,8 +267,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -279,8 +277,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/hisat2/multiqc_report.html").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -316,6 +312,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/general_stats_table.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-cnt.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_pe_plot-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_se_plot-cnt.pdf").name, @@ -325,8 +323,6 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Counts.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_clustering-plot.pdf").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/hisat2_deseq2_pca-plot.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, @@ -372,6 +368,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_pe_plot-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-cnt.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/hisat2_se_plot-pct.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/rseqc_bam_stat.png").name, @@ -392,6 +390,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg").name, @@ -425,6 +425,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name, @@ -463,8 +465,6 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name ).match("multiqc_plots") }, { assert snapshot( // Metrics are not stable @@ -631,36 +631,36 @@ nextflow_pipeline { file("${params.outdir}/hisat2/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("hisat2/rseqc") }, { assert snapshot( - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/hisat2/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("hisat2/samtools_stats") }, { assert snapshot( diff --git a/tests/min_mapped_reads.nf.test b/tests/min_mapped_reads.nf.test index ce5a8b780..dde1c3706 100644 --- a/tests/min_mapped_reads.nf.test +++ b/tests/min_mapped_reads.nf.test @@ -95,9 +95,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), @@ -108,7 +106,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -118,6 +115,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -140,6 +138,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, @@ -159,6 +158,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, @@ -187,8 +187,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -199,8 +197,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -286,26 +282,30 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Events-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_annotation_junctions_plot_Junctions-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_All_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Known_Junctions.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_junction_saturation_plot_Novel_Junctions.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, @@ -670,30 +670,30 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/remove_ribo_rna.nf.test b/tests/remove_ribo_rna.nf.test index f73f98286..430f18b6f 100644 --- a/tests/remove_ribo_rna.nf.test +++ b/tests/remove_ribo_rna.nf.test @@ -94,9 +94,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), @@ -107,7 +105,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -117,17 +114,11 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, - file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt").name, @@ -147,18 +138,27 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_inner_distance_plot_Percentages.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Events.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_annotation_junctions_plot_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_all.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_All_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Known_Junctions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_junction_saturation_plot_Novel_Junctions.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_distribution_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_read_dups_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/sortmerna-detailed-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name @@ -187,8 +187,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -199,8 +197,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/sortmerna-detailed-plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable @@ -289,6 +285,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, @@ -309,6 +307,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, @@ -770,36 +770,36 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/skip_qc.nf.test b/tests/skip_qc.nf.test index 410aa5a1b..8fd703462 100644 --- a/tests/skip_qc.nf.test +++ b/tests/skip_qc.nf.test @@ -63,31 +63,31 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_data.json").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, @@ -104,14 +104,10 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -151,10 +147,14 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png").name, @@ -192,36 +192,36 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg").name ).match("multiqc_plots") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/skip_trimming.nf.test b/tests/skip_trimming.nf.test index 912ebc13f..e5b3aa080 100644 --- a/tests/skip_trimming.nf.test +++ b/tests/skip_trimming.nf.test @@ -60,9 +60,7 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_histogram_2.txt"), @@ -73,7 +71,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt").name, @@ -82,6 +79,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_picard_dups.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -104,6 +102,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/rseqc_bam_stat.txt").name, @@ -123,6 +122,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, @@ -138,8 +138,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), @@ -150,8 +148,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_salmon/multiqc_report.html").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf").name, @@ -216,6 +212,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/rseqc_bam_stat.png").name, @@ -236,6 +234,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png").name, @@ -672,36 +672,36 @@ nextflow_pipeline { file("${params.outdir}/star_salmon/salmon.merged.transcript_tpm.tsv").name ).match("star_salmon/salmon") }, { assert snapshot( - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_salmon/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_salmon/samtools_stats") }, { assert snapshot( diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 94f5d6fd9..0f03bc6db 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -94,23 +94,17 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_featurecounts_biotype_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_histogram_2.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Counts.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_gene_coverage_profile_Normalised.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_cov_hist.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_assignment_plot.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_multimapping_rates.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_infer_experiment_plot.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-idxstats-mapped-reads-plot_Raw_Counts.txt"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt"), // These files are not stable file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt").name, @@ -120,6 +114,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_general_stats.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_picard_dups.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rsem.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_infer_experiment.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt").name, @@ -144,6 +141,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_genomic_origin.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/qualimap_rnaseq_genome_results.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_assignment_plot.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rsem_multimapping_rates.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_bam_stat.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/rseqc_inner_distance_plot_Counts.txt").name, @@ -161,13 +160,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/samtools_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_alignment_plot.txt").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_data/star_summary_table.txt").name ).match("multiqc_data") }, { assert snapshot( - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-cnt.pdf"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-pct.pdf"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_multimapping_rates.pdf"), + path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png"), @@ -191,12 +189,8 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Counts.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_gene_coverage_profile_Normalised.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-pct.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_multimapping_rates.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_infer_experiment_plot.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png"), @@ -206,11 +200,6 @@ nextflow_pipeline { path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png"), path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-cnt.svg"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-pct.svg"), - path("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_multimapping_rates.svg"), // PDFs, SVGs, some PNGs and HTML reports are not stable file("${params.outdir}/multiqc/star_rsem/multiqc_report.html").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-cnt.pdf").name, @@ -252,6 +241,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_gene_coverage_profile_Normalised.pdf").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-cnt.pdf").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/qualimap_genomic_origin-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-cnt.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_assignment_plot-pct.pdf").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rsem_multimapping_rates.pdf").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_bam_stat.pdf").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_infer_experiment_plot.pdf").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_inner_distance_plot_Counts.pdf").name, @@ -295,8 +287,12 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/picard_deduplication-pct.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-cnt.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/qualimap_genomic_origin-pct.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rsem_assignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_bam_stat.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Counts.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/rseqc_inner_distance_plot_Percentages.png").name, @@ -315,6 +311,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-cnt.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_alignment_plot-pct.png").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png").name, @@ -359,6 +357,9 @@ nextflow_pipeline { file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_gene_coverage_profile_Normalised.svg").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-cnt.svg").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/qualimap_genomic_origin-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-cnt.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_assignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rsem_multimapping_rates.svg").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_bam_stat.svg").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_infer_experiment_plot.svg").name, file("${params.outdir}/multiqc/star_rsem/multiqc_report_plots/svg/rseqc_inner_distance_plot_Counts.svg").name, @@ -565,11 +566,12 @@ nextflow_pipeline { file("${params.outdir}/star_rsem/featurecounts/WT_REP2.featureCounts.txt.summary").name ).match("star_rsem/featurecounts") }, { assert snapshot( - path("${params.outdir}/star_rsem/log/RAP1_IAA_30M_REP1.log"), - path("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP1.log"), - path("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP2.log"), - path("${params.outdir}/star_rsem/log/WT_REP1.log"), - path("${params.outdir}/star_rsem/log/WT_REP2.log") + // These files are unstable + file("${params.outdir}/star_rsem/log/RAP1_IAA_30M_REP1.log").name, + file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP1.log").name, + file("${params.outdir}/star_rsem/log/RAP1_UNINDUCED_REP2.log").name, + file("${params.outdir}/star_rsem/log/WT_REP1.log").name, + file("${params.outdir}/star_rsem/log/WT_REP2.log").name ).match("star_rsem/log") }, { assert snapshot( // Metrics are not stable @@ -640,33 +642,34 @@ nextflow_pipeline { { assert snapshot( path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.genes.results"), path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.cnt"), - path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.model"), - path("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.theta"), path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.genes.results"), path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.cnt"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.model"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.theta"), path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.genes.results"), path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.isoforms.results"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.cnt"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.model"), - path("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.theta"), path("${params.outdir}/star_rsem/WT_REP1.genes.results"), path("${params.outdir}/star_rsem/WT_REP1.isoforms.results"), - path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.cnt"), - path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.model"), - path("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.theta"), path("${params.outdir}/star_rsem/WT_REP2.genes.results"), path("${params.outdir}/star_rsem/WT_REP2.isoforms.results"), - path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.cnt"), - path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.model"), - path("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.theta"), path("${params.outdir}/star_rsem/rsem.merged.gene_counts.tsv"), path("${params.outdir}/star_rsem/rsem.merged.gene_tpm.tsv"), path("${params.outdir}/star_rsem/rsem.merged.transcript_counts.tsv"), - path("${params.outdir}/star_rsem/rsem.merged.transcript_tpm.tsv") + path("${params.outdir}/star_rsem/rsem.merged.transcript_tpm.tsv"), + // These files are not stable + file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.cnt").name, + file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.model").name, + file("${params.outdir}/star_rsem/RAP1_IAA_30M_REP1.stat/RAP1_IAA_30M_REP1.theta").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.cnt").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.model").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP1.stat/RAP1_UNINDUCED_REP1.theta").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.cnt").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.model").name, + file("${params.outdir}/star_rsem/RAP1_UNINDUCED_REP2.stat/RAP1_UNINDUCED_REP2.theta").name, + file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.cnt").name, + file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.model").name, + file("${params.outdir}/star_rsem/WT_REP1.stat/WT_REP1.theta").name, + file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.cnt").name, + file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.model").name, + file("${params.outdir}/star_rsem/WT_REP2.stat/WT_REP2.theta").name ).match("star_rsem/rsem") }, { assert snapshot( path("${params.outdir}/star_rsem/rseqc/infer_experiment/RAP1_IAA_30M_REP1.infer_experiment.txt"), @@ -767,36 +770,36 @@ nextflow_pipeline { file("${params.outdir}/star_rsem/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls").name ).match("star_rsem/rseqc") }, { assert snapshot( - path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.flagstat"), - path("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.idxstats"), // These files are not stable + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_IAA_30M_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/RAP1_UNINDUCED_REP2.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/WT_REP1.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.markdup.sorted.bam.stats").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.flagstat").name, + file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.idxstats").name, file("${params.outdir}/star_rsem/samtools_stats/WT_REP2.sorted.bam.stats").name ).match("star_rsem/samtools_stats") }, { assert snapshot( From e4cfa09c0899163863ed5cd9bb06f1a6193a64ae Mon Sep 17 00:00:00 2001 From: maxulysse Date: Mon, 26 Aug 2024 20:03:54 +0200 Subject: [PATCH 41/41] update tests and snapshots --- tests/default.nf.test.snap | 60 ++++----- tests/featurecounts_group_type.nf.test.snap | 60 ++++----- tests/hisat2.nf.test | 8 +- tests/hisat2.nf.test.snap | 72 +++++------ tests/min_mapped_reads.nf.test.snap | 62 +++++----- tests/remove_ribo_rna.nf.test.snap | 76 ++++++------ tests/skip_qc.nf.test.snap | 60 ++++----- tests/skip_trimming.nf.test.snap | 60 ++++----- tests/star_rsem.nf.test.snap | 128 ++++++++++---------- 9 files changed, 293 insertions(+), 293 deletions(-) diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index ba779ac75..e625d1637 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -227,42 +227,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:44:57.974787" + "timestamp": "2024-08-26T18:42:17.143005" }, "Params: default - stub": { "content": [ @@ -320,8 +320,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,4c66fce934b018143e7b8f6a1383d3f6", "featurecounts_biotype_plot-pct.png:md5,9191dc2dd130f22ad404d27e045d2304", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", @@ -332,8 +330,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -417,6 +413,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -437,6 +435,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -519,7 +519,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:21:24.616733" + "timestamp": "2024-08-26T18:42:16.932219" }, "fastqc/raw": { "content": [ @@ -694,9 +694,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -707,7 +705,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -716,6 +713,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -738,6 +736,7 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -757,6 +756,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -764,7 +764,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:21:24.483792" + "timestamp": "2024-08-26T18:42:16.785525" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/featurecounts_group_type.nf.test.snap b/tests/featurecounts_group_type.nf.test.snap index 078ab9d3d..b1160d39d 100644 --- a/tests/featurecounts_group_type.nf.test.snap +++ b/tests/featurecounts_group_type.nf.test.snap @@ -122,9 +122,7 @@ "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -135,7 +133,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -144,6 +141,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -166,6 +164,7 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -185,6 +184,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -192,7 +192,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:29:22.875142" + "timestamp": "2024-08-26T18:50:10.937365" }, "trimgalore": { "content": [ @@ -367,42 +367,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T14:18:39.635582" + "timestamp": "2024-08-26T18:50:11.105038" }, "salmon/deseq2_qc": { "content": [ @@ -469,8 +469,6 @@ "fastqc_sequence_counts_plot-pct.png:md5,55fa5838c8b2db978fcfa5cb83f6b054", "fastqc_sequence_duplication_levels_plot-1.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "qualimap_gene_coverage_profile_Counts.png:md5,ac424dc7e5444a32e482bd5048ac4432", "qualimap_gene_coverage_profile_Normalised.png:md5,62e5a2146daec985b8c2de02e3b57c1e", "rseqc_infer_experiment_plot.png:md5,60c3cafb671fad2cf5f695615230eb8f", @@ -481,8 +479,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -564,6 +560,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -584,6 +582,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -664,7 +664,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:29:22.943986" + "timestamp": "2024-08-26T18:50:11.011282" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/hisat2.nf.test b/tests/hisat2.nf.test index 67ae1187e..9577086ea 100644 --- a/tests/hisat2.nf.test +++ b/tests/hisat2.nf.test @@ -240,8 +240,8 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_data/salmon_plot.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Percentage_of_total.txt").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-flagstat-dp_Read_counts.txt").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name - file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools-stats-dp.txt").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_data/samtools_alignment_plot.txt").name ).match("multiqc_data") }, { assert snapshot( path("${params.outdir}/multiqc/hisat2/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png"), @@ -426,7 +426,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/general_stats_table.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_clustering-plot.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_deseq2_pca-plot.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-cnt.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_pe_plot-pct.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/hisat2_se_plot-cnt.svg").name, @@ -464,7 +464,7 @@ nextflow_pipeline { file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools-stats-dp.svg").name, file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg").name, - file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name, + file("${params.outdir}/multiqc/hisat2/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg").name ).match("multiqc_plots") }, { assert snapshot( // Metrics are not stable diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index c3c508b2e..4e82775d6 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -150,9 +150,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,d35ad008181f0f7be84d5770d17a3a65", - "multiqc_picard_dups.txt:md5,71d5bafee1a4916951349018f387f7a0", "multiqc_samtools_idxstats.txt:md5,66a8e8aecb6233f5a3521151b1ce8d49", - "picard_deduplication.txt:md5,b54a144d4f23ade2221d7ca1af1997f4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -163,7 +161,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3625f666cc09d0f07990716aeccd869f", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,6c323b383a6506d124506405b9463d93", - "samtools_alignment_plot.txt:md5,b6ba3cc94a91b3d0a84c3fa721914744", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "hisat2_pe_plot.txt", @@ -181,6 +178,7 @@ "multiqc_hisat2_deseq2_clustering-plot_3.txt", "multiqc_hisat2_deseq2_clustering-plot_4.txt", "multiqc_hisat2_deseq2_pca-plot.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -196,6 +194,7 @@ "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", @@ -213,13 +212,14 @@ "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", - "samtools-stats-dp.txt" + "samtools-stats-dp.txt", + "samtools_alignment_plot.txt" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:35:09.357006" + "timestamp": "2024-08-26T19:01:52.559836" }, "hisat2/picard_metrics": { "content": [ @@ -277,42 +277,42 @@ }, "hisat2/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e04029ba0b7c9a5007b1e21190416ab3", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,acdfa72b8fb5785abeddaabdab1ed8ca", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,58ac8d961ffe5af5140e597ce46d1ac2", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,b0b719dd29053aa37010082b6a0bb8d1", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,0f82cf321c7ac21d11c29b7e8fd6893b", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,05a67765b944740c60f263a42a5fd65d", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,cb40075ffa2e6f66d8b4b5025fd62004", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,92d7610422de90da2e76f99461721b7f", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,a72f0d10ac28ec362a79435db766251f", - "WT_REP1.markdup.sorted.bam.flagstat:md5,cb3229294e384dba57b00ddab95e5cc9", - "WT_REP1.markdup.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP1.sorted.bam.flagstat:md5,c55ed3c6ea5f4134036fa8a09c20a1ee", - "WT_REP1.sorted.bam.idxstats:md5,93da4c4f281b38c0f783cb4b7e93a6d0", - "WT_REP2.markdup.sorted.bam.flagstat:md5,a0702469e2d220391604e1b72100cad1", - "WT_REP2.markdup.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", - "WT_REP2.sorted.bam.flagstat:md5,b33836e522593ca0aed7c3b10973d5ed", - "WT_REP2.sorted.bam.idxstats:md5,ea45aa47d0b2b85d8aed7072e6ea36b5", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:55:07.609425" + "timestamp": "2024-08-26T19:01:52.753084" }, "salmon/deseq2_qc": { "content": [ @@ -400,8 +400,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,138e00d2fe0af27f2979cf7bdff83b46", "featurecounts_biotype_plot-pct.png:md5,3b7550efe9068f3ada2cc64e311f3338", - "picard_deduplication-cnt.png:md5,fd520fbb1fda9104eb4d39d42df385d0", - "picard_deduplication-pct.png:md5,dbced4008901ab031eda6d0d96ca038b", "qualimap_gene_coverage_profile_Counts.png:md5,1aa39028b017760d0b09f1b6f8c1fa3a", "qualimap_gene_coverage_profile_Normalised.png:md5,1cd382a79b89564a006afe431aa3916d", "rseqc_infer_experiment_plot.png:md5,73f5b860029912da9c3f6a887238d251", @@ -412,8 +410,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,3bb99f72a15a4159860008beea8c802b", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,25015f9be4710c4eccc50f30db3bf521", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,baa90f5ad4d999fc60db30840b72d8c6", - "samtools_alignment_plot-cnt.png:md5,142e06e9daa0fe938f1e9162e1e850a2", - "samtools_alignment_plot-pct.png:md5,bbffb494310e6dff84d9fe7bc99e34fe", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -448,6 +444,8 @@ "featurecounts_biotype_plot-cnt.pdf", "featurecounts_biotype_plot-pct.pdf", "general_stats_table.pdf", + "hisat2_deseq2_clustering-plot.pdf", + "hisat2_deseq2_pca-plot.pdf", "hisat2_pe_plot-cnt.pdf", "hisat2_pe_plot-pct.pdf", "hisat2_se_plot-cnt.pdf", @@ -457,8 +455,6 @@ "qualimap_gene_coverage_profile_Counts.pdf", "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", - "hisat2_deseq2_clustering-plot.pdf", - "hisat2_deseq2_pca-plot.pdf", "qualimap_genomic_origin-pct.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", @@ -504,6 +500,8 @@ "hisat2_pe_plot-pct.png", "hisat2_se_plot-cnt.png", "hisat2_se_plot-pct.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -524,6 +522,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "cutadapt_filtered_reads_plot-cnt.svg", "cutadapt_filtered_reads_plot-pct.svg", "cutadapt_trimmed_sequences_plot_3_Counts.svg", @@ -557,6 +557,8 @@ "featurecounts_biotype_plot-cnt.svg", "featurecounts_biotype_plot-pct.svg", "general_stats_table.svg", + "hisat2_deseq2_clustering-plot.svg", + "hisat2_deseq2_pca-plot.svg", "hisat2_pe_plot-cnt.svg", "hisat2_pe_plot-pct.svg", "hisat2_se_plot-cnt.svg", @@ -594,15 +596,13 @@ "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.svg", "samtools-stats-dp.svg", "samtools_alignment_plot-cnt.svg", - "samtools_alignment_plot-pct.svg", - "hisat2_deseq2_clustering-plot.svg", - "hisat2_deseq2_pca-plot.svg" + "samtools_alignment_plot-pct.svg" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:35:09.426445" + "timestamp": "2024-08-26T19:01:52.649421" }, "fastqc/raw": { "content": [ diff --git a/tests/min_mapped_reads.nf.test.snap b/tests/min_mapped_reads.nf.test.snap index 8d6d24c80..99789ff7c 100644 --- a/tests/min_mapped_reads.nf.test.snap +++ b/tests/min_mapped_reads.nf.test.snap @@ -185,36 +185,36 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:06:37.230258" + "timestamp": "2024-08-26T19:09:21.84327" }, "multiqc_plots": { "content": [ @@ -242,8 +242,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,95b10627fff1af0a209b8e380f4a4d0b", "featurecounts_biotype_plot-pct.png:md5,f9c1cf03824ff9ba7da8537ecd93945b", - "picard_deduplication-cnt.png:md5,b09ea843c14ec1d0370fa56c8ce29e87", - "picard_deduplication-pct.png:md5,6bdbd89afeff028594ad2a5a38e9b2a7", "qualimap_gene_coverage_profile_Counts.png:md5,2d54a60bef3dfa978da48c1b6872c41c", "qualimap_gene_coverage_profile_Normalised.png:md5,a85a901be4c08c9dfcfd9fc87d890c1e", "rseqc_infer_experiment_plot.png:md5,5ce01a7b923f4e6433b76dd88ca22f42", @@ -254,8 +252,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,a6849cd92ae738441212b681a411614d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,4c06988372df63a1fb5f8be93f73ae8f", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -340,26 +336,30 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", - "rseqc_bam_stat.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", + "rseqc_bam_stat.png", + "rseqc_inner_distance_plot_Counts.png", + "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_annotation_junctions_plot_Events-cnt.png", "rseqc_junction_annotation_junctions_plot_Events-pct.png", "rseqc_junction_annotation_junctions_plot_Junctions-cnt.png", "rseqc_junction_annotation_junctions_plot_Junctions-pct.png", - "rseqc_read_distribution_plot-cnt.png", - "rseqc_read_distribution_plot-pct.png", - "rseqc_inner_distance_plot_Counts.png", - "rseqc_inner_distance_plot_Percentages.png", "rseqc_junction_saturation_plot_All_Junctions.png", "rseqc_junction_saturation_plot_Known_Junctions.png", "rseqc_junction_saturation_plot_Novel_Junctions.png", + "rseqc_read_distribution_plot-cnt.png", + "rseqc_read_distribution_plot-pct.png", "salmon_deseq2_clustering-plot.png", "salmon_deseq2_pca-plot.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -443,7 +443,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:42:10.506344" + "timestamp": "2024-08-26T19:09:21.766479" }, "Params: --min_mapped_reads 90 - stub": { "content": [ @@ -634,9 +634,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,f3c566d2eaf6bf2ffe5ad12036ce3500", - "multiqc_picard_dups.txt:md5,6dff325f1bf12d9de88a11af272be755", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,bcf1670f90e552256db4de7fa65d5306", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -647,7 +645,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,01637c600d3840500851eb4118564cc6", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -656,6 +653,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -678,6 +676,7 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -697,6 +696,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -704,7 +704,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:42:10.446106" + "timestamp": "2024-08-26T19:09:21.700284" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/remove_ribo_rna.nf.test.snap b/tests/remove_ribo_rna.nf.test.snap index 9e1c4be55..a90fd3388 100644 --- a/tests/remove_ribo_rna.nf.test.snap +++ b/tests/remove_ribo_rna.nf.test.snap @@ -227,42 +227,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,9cb85f4008ba88f43e15fae47baad525", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,8ac0db45c52a28d167582874992e5833", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,ba4001c9dec79a99b79e3162ba939f85", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,0496e26c6be67b341255761a447b1569", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,12fb0d3b2c65e4738f30d530a329efb1", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,fd9be758f872e026a22b3ed86628daed", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,2df8940452346d9d82b95206d4b304e1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,3535e1cbe40f90e3749dad930251dd9f", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,b42aae33316d4a5a58459143eab2e4f0", - "WT_REP1.markdup.sorted.bam.flagstat:md5,d931e8e7fd82c493d12e78f404b13f2c", - "WT_REP1.markdup.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP1.sorted.bam.flagstat:md5,7bffb4d7dff374febb1ca99c1436ebf7", - "WT_REP1.sorted.bam.idxstats:md5,d2c9dce1a6fcf97a65e3b4313d8a29ef", - "WT_REP2.markdup.sorted.bam.flagstat:md5,ca4330f24cf0d98ceb18c617294aed9e", - "WT_REP2.markdup.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", - "WT_REP2.sorted.bam.flagstat:md5,41d560c31aa88088efffe62d0f488583", - "WT_REP2.sorted.bam.idxstats:md5,47d975efef6048ae120f71124e2b378f", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T13:19:36.4571" + "timestamp": "2024-08-26T19:21:47.319657" }, "multiqc_plots": { "content": [ @@ -289,8 +289,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,ed2c5826034fcf2417afe79902897c45", "featurecounts_biotype_plot-pct.png:md5,96abf028d347f568289b3a741aa8c08d", - "picard_deduplication-cnt.png:md5,015a79422216c364e1d8ae4389b63838", - "picard_deduplication-pct.png:md5,73b0c4736e772c7daeae10f09dd73d21", "qualimap_gene_coverage_profile_Counts.png:md5,fb739f4297a156f0913f21f20090f598", "qualimap_gene_coverage_profile_Normalised.png:md5,710960caa692f0d0eceadcc83650cf00", "rseqc_infer_experiment_plot.png:md5,49f1faa0849545b8a75af2657d0ee5fa", @@ -301,8 +299,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,f12bcf930eac8ed45da7b4668b1169c8", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,ff8e0f61b02f8c9abcce5e83214c87fd", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,1a029e5d23f82d537470363a065b644a", - "samtools_alignment_plot-cnt.png:md5,788eabe2733b62baa802695e558f7198", - "samtools_alignment_plot-pct.png:md5,4c05880be8fd1968d11fb5d621fdac16", "sortmerna-detailed-plot-cnt.png:md5,3875997f21c98e8906cd182d959e0020", "sortmerna-detailed-plot-pct.png:md5,971398875e5cbd50313b6fee7eeb302c", "multiqc_report.html", @@ -390,6 +386,8 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -410,6 +408,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -494,7 +494,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:55:04.146511" + "timestamp": "2024-08-26T19:21:47.217167" }, "Params: --remove_ribo_rna - stub": { "content": [ @@ -700,9 +700,7 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,54f0eef4ab0ecf6a03505b18752b43cd", - "multiqc_picard_dups.txt:md5,5e93e7e4ecaeed2550bffa44dc32184b", "multiqc_samtools_idxstats.txt:md5,413ba06f3d8e4ab0dbde8ef8952c4b32", - "picard_deduplication.txt:md5,32d912bd78e7d99276a52e13575d08aa", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -713,7 +711,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,53addd7b78d8ae224920ec9b97489d72", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,97fc7bde65a7efc5ab3af48ef0400c20", - "samtools_alignment_plot.txt:md5,207e0c3f557679f37350577364b8956d", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -722,17 +719,11 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", + "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", "multiqc_rseqc_read_distribution.txt", - "qualimap_genomic_origin.txt", - "qualimap_rnaseq_genome_results.txt", - "rseqc_bam_stat.txt", - "rseqc_junction_annotation_junctions_plot_Events.txt", - "rseqc_junction_annotation_junctions_plot_Junctions.txt", - "rseqc_read_distribution_plot.txt", - "rseqc_read_dups_plot.txt", - "multiqc_rseqc_infer_experiment.txt", "multiqc_salmon.txt", "multiqc_salmon_deseq2_clustering-plot.txt", "multiqc_salmon_deseq2_clustering-plot_1.txt", @@ -752,18 +743,27 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "picard_deduplication.txt", + "qualimap_genomic_origin.txt", + "qualimap_rnaseq_genome_results.txt", + "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", "rseqc_inner_distance_plot_Percentages.txt", + "rseqc_junction_annotation_junctions_plot_Events.txt", + "rseqc_junction_annotation_junctions_plot_Junctions.txt", "rseqc_junction_saturation_all.txt", "rseqc_junction_saturation_plot_All_Junctions.txt", "rseqc_junction_saturation_plot_Known_Junctions.txt", "rseqc_junction_saturation_plot_Novel_Junctions.txt", + "rseqc_read_distribution_plot.txt", "rseqc_read_dups.txt", + "rseqc_read_dups_plot.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "sortmerna-detailed-plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" @@ -772,7 +772,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T16:55:04.076927" + "timestamp": "2024-08-26T19:21:47.111212" }, "star_salmon/deseq2_qc": { "content": [ diff --git a/tests/skip_qc.nf.test.snap b/tests/skip_qc.nf.test.snap index 514f7b216..397229679 100644 --- a/tests/skip_qc.nf.test.snap +++ b/tests/skip_qc.nf.test.snap @@ -111,30 +111,30 @@ "multiqc_citations.txt:md5,ef51c78faebdd32bad296ba14406b41e", "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", - "multiqc_picard_dups.txt:md5,4f4aca636444de555500207fec553076", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", - "picard_deduplication.txt:md5,35c88deda36f1b3e0ff1ee0799b141d4", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", - "samtools_alignment_plot.txt:md5,32474a6cb875a2a43febb1b9fb33be20", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", "multiqc_data.json", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_salmon.txt", "multiqc_samtools_flagstat.txt", "multiqc_samtools_stats.txt", "multiqc_software_versions.txt", "multiqc_sources.txt", "multiqc_star.txt", + "picard_deduplication.txt", "salmon_plot.txt", "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -142,7 +142,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:57.852981" + "timestamp": "2024-08-26T19:28:48.798947" }, "references": { "content": [ @@ -207,42 +207,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,e3689e1939a931a656ab14b5a40d27a9", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,990280b423241cd1d3e9ab3410841ee8", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,37f5bf17f50d0389b33964438d81afe8", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,30b35c766650cfb3af89fa09c8654b59", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,451eeb9f3caea89d069f26a77a3ac9e9", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,9ef37f60b9192863b3ea595ed8a5c4a1", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,a093ff94182b1cd6a206b019e43c8281", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,d0e0e89c8af100c2adfa7cbf0021f8a2", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,3793df681e37806a931cf359ffbd469d", - "WT_REP1.markdup.sorted.bam.flagstat:md5,501ff3ad52e73a6168814545bb99abf8", - "WT_REP1.markdup.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP1.sorted.bam.flagstat:md5,694fa7255da6612e0503f37b41cdbade", - "WT_REP1.sorted.bam.idxstats:md5,e62dc2e246e11e0e4640db038b857b6f", - "WT_REP2.markdup.sorted.bam.flagstat:md5,3530fb25cc5dfe72cc39053264b3b0cc", - "WT_REP2.markdup.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", - "WT_REP2.sorted.bam.flagstat:md5,e1b514b8f09016ac33e31c25c8e5a447", - "WT_REP2.sorted.bam.idxstats:md5,e8bf92716dc2dbae6c3dbdadefbebc68", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:23:34.122811" + "timestamp": "2024-08-26T19:28:48.898246" }, "salmon": { "content": [ @@ -280,14 +280,10 @@ "fastqc_sequence_counts_plot-cnt.png:md5,2874fea747c7ff46828bf4f17668caf8", "fastqc_sequence_counts_plot-pct.png:md5,0022d7f5ac78b6eff157de24e37c5ab0", "fastqc_sequence_duplication_levels_plot.png:md5,fcd3b1ec2b95fe4bcd607dc28179a754", - "picard_deduplication-cnt.png:md5,52297225fca30daa61d3271754bdbc1a", - "picard_deduplication-pct.png:md5,b2aa123cc65c933ca630d89c6f098550", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png:md5,ce6abb232fd5b5f2e66c0fe9a571d75f", "samtools-idxstats-mapped-reads-plot_Normalised_Counts-log.png:md5,6b44818f886ef020fb3646f152ad4af6", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-cnt.png:md5,d5d8a85b7ad72a0cb93d9283ea12b23f", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", - "samtools_alignment_plot-cnt.png:md5,84f0e82efcef1221c5c2d292b4d4431c", - "samtools_alignment_plot-pct.png:md5,7836b2057272b390f75c890e26034ec2", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -326,10 +322,14 @@ "fastqc_sequence_length_distribution_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "salmon_plot.png", "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_summary_table.png", @@ -370,7 +370,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T12:11:57.881376" + "timestamp": "2024-08-26T19:28:48.850602" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/skip_trimming.nf.test.snap b/tests/skip_trimming.nf.test.snap index 2d36963fa..f71775121 100644 --- a/tests/skip_trimming.nf.test.snap +++ b/tests/skip_trimming.nf.test.snap @@ -108,9 +108,7 @@ "multiqc_citations.txt:md5,1f80cefb6f0103d9a316c396a9441a90", "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_featurecounts_biotype_plot.txt:md5,567475905baa63091cfd0560fb297e10", - "multiqc_picard_dups.txt:md5,825db93f9329a134414feff0a3ce601c", "multiqc_samtools_idxstats.txt:md5,adf5f32fa1485ad0f4dacdfedc7b4bbc", - "picard_deduplication.txt:md5,b14cb08fecb135e93b8dd4e16f9e44fd", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -121,7 +119,6 @@ "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,ae45731d8d4595f77e6b271004f3a070", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a557130553131c893398532377d3b525", - "samtools_alignment_plot.txt:md5,8a3a4dfbbfc068f150836ab6e163424a", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", "junction_saturation_novel.txt", @@ -129,6 +126,7 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -151,6 +149,7 @@ "multiqc_star_salmon_deseq2_clustering-plot_3.txt", "multiqc_star_salmon_deseq2_clustering-plot_4.txt", "multiqc_star_salmon_deseq2_pca-plot.txt", + "picard_deduplication.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", "rseqc_bam_stat.txt", @@ -170,6 +169,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -177,7 +177,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:04:58.433949" + "timestamp": "2024-08-26T19:36:32.752543" }, "star_salmon/rseqc": { "content": [ @@ -364,42 +364,42 @@ }, "star_salmon/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,1c541ffc31671136810db9586f150155", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,cc2766e4a48241322c2528aa61f7d208", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,94c8742a1292d77da53a27c535483247", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,cc2766e4a48241322c2528aa61f7d208", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,083e57d9f4bbb14e0b46622bbaeaae8c", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,e27c453209fefead3f703e3ab1c0b3f7", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,b67e1eb8b5bc947d670ac81ef8f3aeda", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,e27c453209fefead3f703e3ab1c0b3f7", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,36cebb6188f9fd742562493e6a6640fe", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,79cebfe8ad6602dffd2199f5472b28d0", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,ef6a9825af30377b0781a4d4a29b932b", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,79cebfe8ad6602dffd2199f5472b28d0", - "WT_REP1.markdup.sorted.bam.flagstat:md5,6d3457815eb053088f68f84efcd20280", - "WT_REP1.markdup.sorted.bam.idxstats:md5,0da68758394dbc7470b2a2ea50bb8814", - "WT_REP1.sorted.bam.flagstat:md5,b1909dcb78af39009545b03fe1584cc5", - "WT_REP1.sorted.bam.idxstats:md5,0da68758394dbc7470b2a2ea50bb8814", - "WT_REP2.markdup.sorted.bam.flagstat:md5,5cd1d564776bee679329d90de069b2d6", - "WT_REP2.markdup.sorted.bam.idxstats:md5,22d51757c5b252c030984f169a131237", - "WT_REP2.sorted.bam.flagstat:md5,84f3a9290292d1a47ed095616b506ebd", - "WT_REP2.sorted.bam.idxstats:md5,22d51757c5b252c030984f169a131237", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T15:27:30.577354" + "timestamp": "2024-08-26T19:36:32.899658" }, "salmon/deseq2_qc": { "content": [ @@ -456,8 +456,6 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,dcb37b4ce2fff5ca2e22767b172e55a8", "featurecounts_biotype_plot-pct.png:md5,b15370ba2c056815939251f820d9e2af", - "picard_deduplication-cnt.png:md5,e01e21b8894cdc3c540d82619aa66f62", - "picard_deduplication-pct.png:md5,b6cb33b941cbc71c22167d01d61b38f8", "qualimap_gene_coverage_profile_Counts.png:md5,8312f777db61509caa66d1f53a4b6b07", "qualimap_gene_coverage_profile_Normalised.png:md5,66acb12427130766801a8376f95ed88b", "rseqc_infer_experiment_plot.png:md5,c3108e35020ee93a77a62ea0167613b2", @@ -468,8 +466,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,19317ad8f1448cd7eb1d319f85cc5c4d", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,64f2501f91db6dd0edd5e49c0b9ca8b7", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,52f30fc3448f43735ce9eca54b306c8e", - "samtools_alignment_plot-cnt.png:md5,267822d4de67c0c7bc543c704bec1cbe", - "samtools_alignment_plot-pct.png:md5,17f1dbee7ed2fa1039596175d9f34b42", "multiqc_report.html", "dupradar-section-plot.pdf", "fail_strand_check_table.pdf", @@ -533,6 +529,8 @@ "fastqc_per_base_sequence_quality_plot.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", "rseqc_bam_stat.png", @@ -553,6 +551,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_salmon_deseq2_clustering-plot.png", @@ -619,7 +619,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:04:58.556659" + "timestamp": "2024-08-26T19:36:32.816392" }, "star_salmon/picard_metrics": { "content": [ diff --git a/tests/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index beefc9b53..4d66a38db 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -82,23 +82,17 @@ "multiqc_fastqc_fastqc_raw.txt:md5,81c3c1a2575a1891a7f2a9637a0f2cc0", "multiqc_fastqc_fastqc_trimmed.txt:md5,a3238f515e01d158d875d69968753804", "multiqc_featurecounts_biotype_plot.txt:md5,27bb37d346e8f0960c882a3676e219e8", - "multiqc_picard_dups.txt:md5,0e258d3ce451fa5233c81a631c807636", - "multiqc_rsem.txt:md5,426cfb38a96c0d7111336be3164171fb", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "picard_deduplication.txt:md5,b6e23251b2007c0759c347aaa31d2a76", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_1.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "picard_histogram_2.txt:md5,d41d8cd98f00b204e9800998ecf8427e", "qualimap_gene_coverage_profile_Counts.txt:md5,387c07f2a93e3d13048c4cd788d1fcc3", "qualimap_gene_coverage_profile_Normalised.txt:md5,35f0b71796622269bc51cf1e7a0650ab", "qualimap_rnaseq_cov_hist.txt:md5,a620cb9d1878e86e10e87500e98122f1", - "rsem_assignment_plot.txt:md5,136b1ca144da9a1b304ff3471ff44390", - "rsem_multimapping_rates.txt:md5,5d91bb56472834622e81e7919f746250", "rseqc_infer_experiment_plot.txt:md5,c0ddf72b026cdc54ad03e75eaa636f7e", "samtools-idxstats-mapped-reads-plot_Normalised_Counts.txt:md5,75acd04232d1804b5f960ee4c5db4722", "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts.txt:md5,3e67e07b5c978fa363965e8e90356eef", "samtools-idxstats-mapped-reads-plot_Raw_Counts.txt:md5,a83e44c5a22e014d377c41419175784c", - "samtools_alignment_plot.txt:md5,911758be5fed6e87b16b288caa39db8e", "fastqc_top_overrepresented_sequences_table-1.txt", "fastqc_top_overrepresented_sequences_table.txt", "junction_saturation_known.txt", @@ -107,6 +101,9 @@ "multiqc_dupradar-section-plot.txt", "multiqc_fail_strand_check_table.txt", "multiqc_general_stats.txt", + "multiqc_picard_dups.txt", + "picard_deduplication.txt", + "multiqc_rsem.txt", "multiqc_rseqc_bam_stat.txt", "multiqc_rseqc_infer_experiment.txt", "multiqc_rseqc_junction_annotation.txt", @@ -131,6 +128,8 @@ "multiqc_star_rsem_deseq2_pca-plot.txt", "qualimap_genomic_origin.txt", "qualimap_rnaseq_genome_results.txt", + "rsem_assignment_plot.txt", + "rsem_multimapping_rates.txt", "rseqc_bam_stat.txt", "rseqc_inner_distance.txt", "rseqc_inner_distance_plot_Counts.txt", @@ -148,6 +147,7 @@ "samtools-flagstat-dp_Percentage_of_total.txt", "samtools-flagstat-dp_Read_counts.txt", "samtools-stats-dp.txt", + "samtools_alignment_plot.txt", "star_alignment_plot.txt", "star_summary_table.txt" ], @@ -155,46 +155,46 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.036713" + "timestamp": "2024-08-26T19:43:20.562966" }, "star_rsem/samtools_stats": { "content": [ - "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat:md5,b4655647adf50bc443313ad150fe2afb", - "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats:md5,99f719593d131af1a215fbb5032acc1e", - "RAP1_IAA_30M_REP1.sorted.bam.flagstat:md5,c2f5d38f0b54990850f4aee711080c99", - "RAP1_IAA_30M_REP1.sorted.bam.idxstats:md5,99f719593d131af1a215fbb5032acc1e", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat:md5,8678d9c4f5280b7b2f7a69034c240551", - "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats:md5,d33f03663678f3c9a063a9cf55b1b1ec", - "RAP1_UNINDUCED_REP1.sorted.bam.flagstat:md5,25e061e1ffb777d0f7f405ffd26533b8", - "RAP1_UNINDUCED_REP1.sorted.bam.idxstats:md5,d33f03663678f3c9a063a9cf55b1b1ec", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat:md5,df6f55cec42df6fdf56f768af3cb8d24", - "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats:md5,37150ce5f3ee6d27ef1994a285ecf7be", - "RAP1_UNINDUCED_REP2.sorted.bam.flagstat:md5,4a55cc0140668a8d572e820159cecf55", - "RAP1_UNINDUCED_REP2.sorted.bam.idxstats:md5,37150ce5f3ee6d27ef1994a285ecf7be", - "WT_REP1.markdup.sorted.bam.flagstat:md5,35022e2aa70234da8122867da4207ccf", - "WT_REP1.markdup.sorted.bam.idxstats:md5,7be99ac4f46a81fa42302aea5da5db8e", - "WT_REP1.sorted.bam.flagstat:md5,afc212aa6cc3394a49d0c550ef202df5", - "WT_REP1.sorted.bam.idxstats:md5,7be99ac4f46a81fa42302aea5da5db8e", - "WT_REP2.markdup.sorted.bam.flagstat:md5,5d24f4ee7aef04aee46c2870c7b0d5c9", - "WT_REP2.markdup.sorted.bam.idxstats:md5,7cccd0ecf83b400e7da8afa93018749b", - "WT_REP2.sorted.bam.flagstat:md5,455fd491f2740a12f56fff9c9af44512", - "WT_REP2.sorted.bam.idxstats:md5,7cccd0ecf83b400e7da8afa93018749b", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.markdup.sorted.bam.stats", + "RAP1_IAA_30M_REP1.sorted.bam.flagstat", + "RAP1_IAA_30M_REP1.sorted.bam.idxstats", "RAP1_IAA_30M_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP1.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP1.sorted.bam.idxstats", "RAP1_UNINDUCED_REP1.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.markdup.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.markdup.sorted.bam.stats", + "RAP1_UNINDUCED_REP2.sorted.bam.flagstat", + "RAP1_UNINDUCED_REP2.sorted.bam.idxstats", "RAP1_UNINDUCED_REP2.sorted.bam.stats", + "WT_REP1.markdup.sorted.bam.flagstat", + "WT_REP1.markdup.sorted.bam.idxstats", "WT_REP1.markdup.sorted.bam.stats", + "WT_REP1.sorted.bam.flagstat", + "WT_REP1.sorted.bam.idxstats", "WT_REP1.sorted.bam.stats", + "WT_REP2.markdup.sorted.bam.flagstat", + "WT_REP2.markdup.sorted.bam.idxstats", "WT_REP2.markdup.sorted.bam.stats", + "WT_REP2.sorted.bam.flagstat", + "WT_REP2.sorted.bam.idxstats", "WT_REP2.sorted.bam.stats" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.566101" + "timestamp": "2024-08-26T19:43:21.034611" }, "trimgalore": { "content": [ @@ -289,39 +289,39 @@ "content": [ "RAP1_IAA_30M_REP1.genes.results:md5,9f76f2687983812c29b108b1faadbb92", "RAP1_IAA_30M_REP1.isoforms.results:md5,7e8af74655cfa3533cdd8de305f101a4", - "RAP1_IAA_30M_REP1.cnt:md5,0dd947319d4be61a70c0972a341df022", - "RAP1_IAA_30M_REP1.model:md5,1f58eab071b48d7dd3563bf1cc49262f", - "RAP1_IAA_30M_REP1.theta:md5,75f1d4cd262c6f668e9851cc399d96be", "RAP1_UNINDUCED_REP1.genes.results:md5,0ebfda99b1e92d071d3d8f12f37d25cd", "RAP1_UNINDUCED_REP1.isoforms.results:md5,5fe29701e388c9ac813ab0e8f02e1e9b", - "RAP1_UNINDUCED_REP1.cnt:md5,722a818544a56ed0d86c2370831ecb18", - "RAP1_UNINDUCED_REP1.model:md5,262576fb8671db5c7debb045040c274a", - "RAP1_UNINDUCED_REP1.theta:md5,94a87800469746b15e219bb68c65f905", "RAP1_UNINDUCED_REP2.genes.results:md5,e6bed419600f1bdc30c59f2c2f0beec3", "RAP1_UNINDUCED_REP2.isoforms.results:md5,35ede7929d359424798d92398d6d9518", - "RAP1_UNINDUCED_REP2.cnt:md5,fa6b94589d49e68e53c19dee98d4f27b", - "RAP1_UNINDUCED_REP2.model:md5,34fb5bf5adf3a9e7ebee83533697dc88", - "RAP1_UNINDUCED_REP2.theta:md5,bd7a159324dc692dcc8ec7bec78167d9", "WT_REP1.genes.results:md5,8cd8c1d87970dbae9983250530a5915d", "WT_REP1.isoforms.results:md5,993a65e02daecd9457c529d118b6e8ac", - "WT_REP1.cnt:md5,938a5d93e8900fcf0771cbb9c6bdc33c", - "WT_REP1.model:md5,752de4891bcbba0072ca1966191fd8fc", - "WT_REP1.theta:md5,2a22bcd7d927e558c55a339ca18c2fe9", "WT_REP2.genes.results:md5,78387c8f57175756fda9c153790f3d37", "WT_REP2.isoforms.results:md5,89bd225b6702ec3edbe13d9443fce40f", - "WT_REP2.cnt:md5,667a6095dc7317aef8bc44d624dee544", - "WT_REP2.model:md5,d416932acda320ec20af45203c6038e9", - "WT_REP2.theta:md5,fe675b73daeca53bb506a009cca2efb6", "rsem.merged.gene_counts.tsv:md5,47f272199f24af4473c959df2a9149dc", "rsem.merged.gene_tpm.tsv:md5,a197b2d131dea75a83f9c219c23fb7a0", "rsem.merged.transcript_counts.tsv:md5,ffc75fd409d75edf5209e8e1af8ec8fc", - "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5" + "rsem.merged.transcript_tpm.tsv:md5,b836618c69d111edf635ce7244ee85e5", + "RAP1_IAA_30M_REP1.cnt", + "RAP1_IAA_30M_REP1.model", + "RAP1_IAA_30M_REP1.theta", + "RAP1_UNINDUCED_REP1.cnt", + "RAP1_UNINDUCED_REP1.model", + "RAP1_UNINDUCED_REP1.theta", + "RAP1_UNINDUCED_REP2.cnt", + "RAP1_UNINDUCED_REP2.model", + "RAP1_UNINDUCED_REP2.theta", + "WT_REP1.cnt", + "WT_REP1.model", + "WT_REP1.theta", + "WT_REP2.cnt", + "WT_REP2.model", + "WT_REP2.theta" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.442121" + "timestamp": "2024-08-26T19:43:20.906583" }, "star_rsem/stringtie": { "content": [ @@ -374,9 +374,6 @@ }, "multiqc_plots": { "content": [ - "rsem_assignment_plot-cnt.pdf:md5,a1673a928363f38e45e3a1327338d367", - "rsem_assignment_plot-pct.pdf:md5,ce967bcc84c0a23c441514e51d759c16", - "rsem_multimapping_rates.pdf:md5,bace39413eb0e6143dd105dc503c8bb4", "cutadapt_filtered_reads_plot-cnt.png:md5,704cf0d91bfa3dd658dd8c9590f669a2", "cutadapt_filtered_reads_plot-pct.png:md5,2684d8b2afca3300e5786486b80237f0", "cutadapt_trimmed_sequences_plot_3_Counts.png:md5,bef41d894629b0c4dab4478bbf197f50", @@ -400,12 +397,8 @@ "fastqc_sequence_duplication_levels_plot.png:md5,747431f0f38f8e4c41a11a072fa18780", "featurecounts_biotype_plot-cnt.png:md5,b033cedf28f1b3f6f48f1ed793160679", "featurecounts_biotype_plot-pct.png:md5,1921c3931d871f8326a6a6c5c8278815", - "picard_deduplication-cnt.png:md5,a0e470143af7da76943152badf83ef1d", - "picard_deduplication-pct.png:md5,250f89fa9407e7cc8d467de6b212dff8", "qualimap_gene_coverage_profile_Counts.png:md5,04a262d5af169d6d771e48555adab37e", "qualimap_gene_coverage_profile_Normalised.png:md5,3bddc4f2a7d462996628e33daf490247", - "rsem_assignment_plot-cnt.png:md5,15fd495eeee0d791d8fe663c9a981b6a", - "rsem_assignment_plot-pct.png:md5,e38d64af2acd404fcdb72a55a6dd1986", "rsem_multimapping_rates.png:md5,e93d35b86e1be681eae9b6ad19e12350", "rseqc_infer_experiment_plot.png:md5,1a3a792e9a6e0c0f93c082594b24e566", "rseqc_read_dups_plot.png:md5,b79c01ce4697ebb7e0ebb4a3da5b44f7", @@ -415,11 +408,6 @@ "samtools-idxstats-mapped-reads-plot_Observed_over_Expected_Counts-log.png:md5,10d7c1023bcf922ac45e653a58ee13c8", "samtools-idxstats-mapped-reads-plot_Raw_Counts-cnt.png:md5,2edc4372d981aacfceb4f16da598d63a", "samtools-idxstats-mapped-reads-plot_Raw_Counts-log.png:md5,5d2286a4f77000c199ed22517338da4a", - "samtools_alignment_plot-cnt.png:md5,4640ff5819853aae35a7972dda40f6ab", - "samtools_alignment_plot-pct.png:md5,092bda5422215c1d2d7797e38802e599", - "rsem_assignment_plot-cnt.svg:md5,1791d7a84262b0299a8b81af0ac4eb59", - "rsem_assignment_plot-pct.svg:md5,64d6c83c006863f891689fcd535545b8", - "rsem_multimapping_rates.svg:md5,91e5caa077ff8ec40609d4b8f74daaf5", "multiqc_report.html", "cutadapt_filtered_reads_plot-cnt.pdf", "cutadapt_filtered_reads_plot-pct.pdf", @@ -460,6 +448,9 @@ "qualimap_gene_coverage_profile_Normalised.pdf", "qualimap_genomic_origin-cnt.pdf", "qualimap_genomic_origin-pct.pdf", + "rsem_assignment_plot-cnt.pdf", + "rsem_assignment_plot-pct.pdf", + "rsem_multimapping_rates.pdf", "rseqc_bam_stat.pdf", "rseqc_infer_experiment_plot.pdf", "rseqc_inner_distance_plot_Counts.pdf", @@ -503,8 +494,12 @@ "fastqc_top_overrepresented_sequences_table-1.png", "fastqc_top_overrepresented_sequences_table.png", "general_stats_table.png", + "picard_deduplication-cnt.png", + "picard_deduplication-pct.png", "qualimap_genomic_origin-cnt.png", "qualimap_genomic_origin-pct.png", + "rsem_assignment_plot-cnt.png", + "rsem_assignment_plot-pct.png", "rseqc_bam_stat.png", "rseqc_inner_distance_plot_Counts.png", "rseqc_inner_distance_plot_Percentages.png", @@ -523,6 +518,8 @@ "samtools-flagstat-dp_Percentage_of_total.png", "samtools-flagstat-dp_Read_counts.png", "samtools-stats-dp.png", + "samtools_alignment_plot-cnt.png", + "samtools_alignment_plot-pct.png", "star_alignment_plot-cnt.png", "star_alignment_plot-pct.png", "star_rsem_deseq2_clustering-plot.png", @@ -567,6 +564,9 @@ "qualimap_gene_coverage_profile_Normalised.svg", "qualimap_genomic_origin-cnt.svg", "qualimap_genomic_origin-pct.svg", + "rsem_assignment_plot-cnt.svg", + "rsem_assignment_plot-pct.svg", + "rsem_multimapping_rates.svg", "rseqc_bam_stat.svg", "rseqc_infer_experiment_plot.svg", "rseqc_inner_distance_plot_Counts.svg", @@ -605,7 +605,7 @@ "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.178293" + "timestamp": "2024-08-26T19:43:20.672077" }, "star_rsem/picard_metrics": { "content": [ @@ -752,17 +752,17 @@ }, "star_rsem/log": { "content": [ - "RAP1_IAA_30M_REP1.log:md5,9b52ef81b57686c41c63d0d53c1a72d5", - "RAP1_UNINDUCED_REP1.log:md5,f0f9f92d686ce202ee464329a56b1f46", - "RAP1_UNINDUCED_REP2.log:md5,c9d68358d6f21024cb235b7191fa8290", - "WT_REP1.log:md5,cd3e07d999a1c8ffbce0a152004b7a12", - "WT_REP2.log:md5,39695fc38849c701844116f3209ccefc" + "RAP1_IAA_30M_REP1.log", + "RAP1_UNINDUCED_REP1.log", + "RAP1_UNINDUCED_REP2.log", + "WT_REP1.log", + "WT_REP2.log" ], "meta": { "nf-test": "0.9.0", "nextflow": "24.04.4" }, - "timestamp": "2024-08-26T17:38:04.313526" + "timestamp": "2024-08-26T19:43:20.787774" }, "Params: --aligner star_rsem - stub": { "content": [