From 2ce830b881c3a0bbbbde8de30456aa82b28f7529 Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 09:51:59 +0200 Subject: [PATCH] update default tests --- tests/default.nf.test | 18 +- tests/default.nf.test.snap | 416 ++++++++++++++----------------------- 2 files changed, 164 insertions(+), 270 deletions(-) diff --git a/tests/default.nf.test b/tests/default.nf.test index 80b19646a..998e136d8 100644 --- a/tests/default.nf.test +++ b/tests/default.nf.test @@ -13,9 +13,11 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') + // bam_files: All bam files + def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam']) assertAll( { assert workflow.success}, { assert snapshot( @@ -24,9 +26,11 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents - stable_path + stable_path, + // All bam files + bam_files.collect{ file -> [ file.getName(), bam(file.toString()).getReadsMD5() ] } ).match() } ) } @@ -44,9 +48,9 @@ nextflow_pipeline { then { // stable_name: All files + folders in ${params.outdir}/ with a stable name - def stable_name = getAllFilesFromDir(params.outdir, true, ['pipeline_info/*.{html,json,txt}'], null) + def stable_name = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}']) // stable_path: All files in ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -55,7 +59,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"), // All stable path name, with a relative path - getRelativePath(stable_name, outputDir), + stable_name, // All files with stable contents stable_path ).match() } diff --git a/tests/default.nf.test.snap b/tests/default.nf.test.snap index 5bddc1cff..7ed40b6cc 100644 --- a/tests/default.nf.test.snap +++ b/tests/default.nf.test.snap @@ -83,14 +83,15 @@ ], [ "genome_transcriptome.fasta:md5,d41d8cd98f00b204e9800998ecf8427e", - "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e" + "genome_transcriptome.gtf:md5,d41d8cd98f00b204e9800998ecf8427e", + "multiqc_plots:md5,d41d8cd98f00b204e9800998ecf8427e" ] ], "meta": { "nf-test": "0.9.0", - "nextflow": "24.04.4" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T07:30:25.608093" + "timestamp": "2024-10-10T09:21:27.152841" }, "Params: default": { "content": [ @@ -283,34 +284,35 @@ "multiqc/star_salmon/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_salmon/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_salmon/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_salmon/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_salmon/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc.log", "multiqc/star_salmon/multiqc_report_data/multiqc_citations.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_data.json", - "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -322,24 +324,16 @@ "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_salmon/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_sources.txt", "multiqc/star_salmon/multiqc_report_data/multiqc_star.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_salmon/multiqc_report_data/multiqc_star_salmon_deseq2_pca-plot.txt", "multiqc/star_salmon/multiqc_report_data/picard_deduplication.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram.txt", "multiqc/star_salmon/multiqc_report_data/picard_histogram_1.txt", @@ -379,32 +373,32 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -428,9 +422,8 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_salmon/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -444,40 +437,38 @@ "multiqc/star_salmon/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-cnt.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_alignment_plot-pct.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_clustering-plot.pdf", - "multiqc/star_salmon/multiqc_report_plots/pdf/star_salmon_deseq2_pca-plot.pdf", "multiqc/star_salmon/multiqc_report_plots/pdf/star_summary_table.pdf", "multiqc/star_salmon/multiqc_report_plots/png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_salmon/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_salmon/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/dupradar.png", "multiqc/star_salmon/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_salmon/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/general_stats_table.png", @@ -501,9 +492,8 @@ "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_salmon/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_salmon/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -517,40 +507,38 @@ "multiqc/star_salmon/multiqc_report_plots/png/samtools_alignment_plot-pct.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-cnt.png", "multiqc/star_salmon/multiqc_report_plots/png/star_alignment_plot-pct.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_clustering-plot.png", - "multiqc/star_salmon/multiqc_report_plots/png/star_salmon_deseq2_pca-plot.png", "multiqc/star_salmon/multiqc_report_plots/png/star_summary_table.png", "multiqc/star_salmon/multiqc_report_plots/svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/general_stats_table.svg", @@ -574,9 +562,8 @@ "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_salmon/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_salmon/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -590,8 +577,6 @@ "multiqc/star_salmon/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-cnt.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_alignment_plot-pct.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_clustering-plot.svg", - "multiqc/star_salmon/multiqc_report_plots/svg/star_salmon_deseq2_pca-plot.svg", "multiqc/star_salmon/multiqc_report_plots/svg/star_summary_table.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", @@ -1301,33 +1286,34 @@ [ "genome_gfp.fasta:md5,e23e302af63736a199985a169fdac055", "genome_gfp.gtf:md5,c98b12c302f15731bfc36bcf297cfe28", - "cutadapt_filtered_reads_plot.txt:md5,bf033e64e9d23bee85b6277f11c663f1", + "cutadapt_filtered_reads_plot.txt:md5,6fa381627f7c1f664f3d4b2cb79cce90", "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_raw-status-check-heatmap.txt:md5,5a89b0d8d162f6b1dbdaf39457bbc03b", + "fastqc_raw_adapter_content_plot.txt:md5,da0389be84cfdd189b1d045212eb2974", + "fastqc_raw_overrepresented_sequences_plot.txt:md5,25d88ea8a72f55e8a374ae802bc7f0b1", + "fastqc_raw_per_base_n_content_plot.txt:md5,d368d7e36ca2f73dcde61f2b486d8213", + "fastqc_raw_per_base_sequence_quality_plot.txt:md5,5c3065b549129702b185ea1b817da420", + "fastqc_raw_per_sequence_gc_content_plot_Counts.txt:md5,9ddaa50167117d3c9188ccf015427704", + "fastqc_raw_per_sequence_gc_content_plot_Percentages.txt:md5,f10ee2881b61308af35f304aa3d810a3", + "fastqc_raw_per_sequence_quality_scores_plot.txt:md5,b5f9a02933e3065952237afd2ec9ce82", + "fastqc_raw_sequence_counts_plot.txt:md5,cbae4979d5db66d3b894abcf8d1c453c", + "fastqc_raw_sequence_duplication_levels_plot.txt:md5,8812cee16f6ca65e2c33635754de1772", + "fastqc_raw_top_overrepresented_sequences_table.txt:md5,43d63c7c7f038becc6b5ef164b2e5f71", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", + "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", + "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", + "fastqc_trimmed_per_base_n_content_plot.txt:md5,418610c1ce119cb786ad434db75d366e", + "fastqc_trimmed_per_base_sequence_quality_plot.txt:md5,bd22e06e41c096ad4f745d40fe96a1e5", + "fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt:md5,004c60768ceb6197765154e3eaa37b7a", + "fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt:md5,95d29060b687f745288ad1ec47750037", + "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c", + "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3", + "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874", "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_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233", "multiqc_featurecounts_biotype_plot.txt:md5,56be7f0813c3cbea0f68f61d9b355b71", "multiqc_samtools_idxstats.txt:md5,fd7d03a91f0b9e01a6939941f7f2243f", "picard_histogram.txt:md5,d41d8cd98f00b204e9800998ecf8427e", @@ -1340,39 +1326,6 @@ "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", - "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", - 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"nextflow": "24.08.0" + "nextflow": "24.09.0" }, - "timestamp": "2024-10-02T08:39:09.000328" + "timestamp": "2024-10-10T09:48:14.477734" } -} +} \ No newline at end of file