From a93e9bbe7f2f42d8bebf7b170323fbbc3dddbc4d Mon Sep 17 00:00:00 2001 From: maxulysse Date: Thu, 10 Oct 2024 12:49:45 +0200 Subject: [PATCH] update last snapshots --- tests/.nftignore | 54 ++--- tests/hisat2.nf.test.snap | 11 +- tests/star_rsem.nf.test | 12 +- tests/star_rsem.nf.test.snap | 396 ++++++++++++----------------------- 4 files changed, 170 insertions(+), 303 deletions(-) diff --git a/tests/.nftignore b/tests/.nftignore index b8f4c7d25..607d912d5 100644 --- a/tests/.nftignore +++ b/tests/.nftignore @@ -1,5 +1,6 @@ bbsplit/*.stats.txt fastqc/*/*.{html,zip} +hisat2/log/*.hisat2.summary.log kallisto/*/abundance.{h5,tsv} kallisto/*/kallisto_quant.log kallisto/*/run_info.json @@ -9,26 +10,29 @@ multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt pipeline_info/*.{html,json,txt,yml} sortmerna/*.sortmerna.log +star_rsem/*.stat/*.{cnt,model,theta} +star_rsem/*.{genes,isoforms}.results +star_rsem/log/*.log star_salmon/log/*.Log.{final.out,out,progress.out} trimgalore/*fastq.gz_trimming_report.txt -{hisat2,star_salmon}/*.{bam,bam.bai} -{hisat2,star_salmon}/bigwig/*.{forward,reverse}.bigWig -{hisat2,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf -{hisat2,star_salmon}/dupradar/histogram/*_expressionHist.pdf -{hisat2,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf -{hisat2,star_salmon}/featurecounts/*.featureCounts.txt.summary -{hisat2,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt -{hisat2,star_salmon}/qualimap/*/css/* -{hisat2,star_salmon}/qualimap/*/images_qualimapReport/* -{hisat2,star_salmon}/qualimap/*/qualimapReport.html -{hisat2,star_salmon}/qualimap/*/rnaseq_qc_results.txt -{hisat2,star_salmon}/rseqc/bam_stat/*.bam_stat.txt -{hisat2,star_salmon}/rseqc/read_distribution/*.read_distribution.txt -{hisat2,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* -{hisat2,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} -{hisat2,star_salmon}/stringtie/*.ballgown/t_data.ctab -{hisat2,star_salmon}/stringtie/*.gene.abundance.txt -{hisat2,star_salmon}/stringtie/*.{coverage,transcripts}.gtf +{hisat2,star_rsem,star_salmon}/*.{bam,bam.bai} +{hisat2,star_rsem,star_salmon}/bigwig/*.{forward,reverse}.bigWig +{hisat2,star_rsem,star_salmon}/dupradar/box_plot/*_duprateExpBoxplot.pdf +{hisat2,star_rsem,star_salmon}/dupradar/histogram/*_expressionHist.pdf +{hisat2,star_rsem,star_salmon}/dupradar/scatter_plot/*_duprateExpDens.pdf +{hisat2,star_rsem,star_salmon}/featurecounts/*.featureCounts.txt.summary +{hisat2,star_rsem,star_salmon}/picard_metrics/*.MarkDuplicates.metrics.txt +{hisat2,star_rsem,star_salmon}/qualimap/*/css/* +{hisat2,star_rsem,star_salmon}/qualimap/*/images_qualimapReport/* +{hisat2,star_rsem,star_salmon}/qualimap/*/qualimapReport.html +{hisat2,star_rsem,star_salmon}/qualimap/*/rnaseq_qc_results.txt +{hisat2,star_rsem,star_salmon}/rseqc/bam_stat/*.bam_stat.txt +{hisat2,star_rsem,star_salmon}/rseqc/read_distribution/*.read_distribution.txt +{hisat2,star_rsem,star_salmon}/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/* +{hisat2,star_rsem,star_salmon}/samtools_stats/*.bam.{flagstat,idxstats,stats} +{hisat2,star_rsem,star_salmon}/stringtie/*.ballgown/t_data.ctab +{hisat2,star_rsem,star_salmon}/stringtie/*.gene.abundance.txt +{hisat2,star_rsem,star_salmon}/stringtie/*.{coverage,transcripts}.gtf {multiqc,multiqc/**}/multiqc_report.html {multiqc,multiqc/**}/multiqc_report_data/fastqc_{raw,trimmed}_top_overrepresented_sequences_table.txt {multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt @@ -41,6 +45,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_general_stats.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_kallisto.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_picard_dups.txt +{multiqc,multiqc/**}/multiqc_report_data/multiqc_rsem.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_bam_stat.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt {multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt @@ -55,6 +60,7 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_genomic_origin.txt {multiqc,multiqc/**}/multiqc_report_data/qualimap_rnaseq_genome_results.txt +{multiqc,multiqc/**}/multiqc_report_data/rsem_assignment_plot.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_bam_stat.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt {multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt @@ -67,16 +73,16 @@ trimgalore/*fastq.gz_trimming_report.txt {multiqc,multiqc/**}/multiqc_report_data/star_alignment_plot.txt {multiqc,multiqc/**}/multiqc_report_data/star_summary_table.txt {multiqc,multiqc/**}/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg} +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.dds.RData +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.pca.vals.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.plots.pdf +{salmon,star_rsem,star_salmon}/deseq2_qc/deseq2.sample.dists.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/*.txt +{salmon,star_rsem,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData {salmon,star_salmon}/*/aux_info/fld.gz {salmon,star_salmon}/*/aux_info/meta_info.json {salmon,star_salmon}/*/libParams/flenDist.txt {salmon,star_salmon}/*/logs/salmon_quant.log {salmon,star_salmon}/*/quant.genes.sf {salmon,star_salmon}/*/quant.sf -{salmon,star_salmon}/deseq2_qc/deseq2.dds.RData -{salmon,star_salmon}/deseq2_qc/deseq2.pca.vals.txt -{salmon,star_salmon}/deseq2_qc/deseq2.plots.pdf -{salmon,star_salmon}/deseq2_qc/deseq2.sample.dists.txt -{salmon,star_salmon}/deseq2_qc/size_factors/*.txt -{salmon,star_salmon}/deseq2_qc/size_factors/deseq2.size_factors.RData {salmon,star_salmon}/salmon.* diff --git a/tests/hisat2.nf.test.snap b/tests/hisat2.nf.test.snap index 9de57ae81..2fec710ac 100644 --- a/tests/hisat2.nf.test.snap +++ b/tests/hisat2.nf.test.snap @@ -761,6 +761,7 @@ "multiqc/hisat2/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/hisat2/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/hisat2/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", "multiqc/hisat2/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", @@ -1192,11 +1193,6 @@ "WT_REP2.biotype_counts_mqc.tsv:md5,74a5436a716a7d99f425f73914cb2794", "WT_REP2.biotype_counts_rrna_mqc.tsv:md5,12294618fe44df1e7f39348372dcb481", "WT_REP2.featureCounts.txt:md5,702446d50a5019c84fcef85d1cfef78c", - "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,e622496abff3ce68afcd1c21a7a1e0df", "coverage_profile_along_genes_(high).txt:md5,b56043c3546cac003461c57abad93536", "coverage_profile_along_genes_(low).txt:md5,1b55d86defcc541643137497c4c6bb06", "coverage_profile_along_genes_(total).txt:md5,1b55d86defcc541643137497c4c6bb06", @@ -1250,7 +1246,6 @@ "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,b2c138ad689c01aaae91b5850112a964", "fastqc_sequence_length_distribution_plot.txt:md5,6fe2c985606abad947bcca99b015ae33", "fastqc_trimmed-status-check-heatmap.txt:md5,22a03548736b88b23be6bc0c9ef1b4a6", "fastqc_trimmed_overrepresented_sequences_plot.txt:md5,4adfeacd3a3a6c7c808f121b24e6b247", @@ -1315,6 +1310,6 @@ "nf-test": "0.9.0", "nextflow": "24.09.0" }, - "timestamp": "2024-10-10T10:25:14.209047" + "timestamp": "2024-10-10T12:37:31.888584" } -} +} \ No newline at end of file diff --git a/tests/star_rsem.nf.test b/tests/star_rsem.nf.test index 268a1fabb..8c52fb826 100644 --- a/tests/star_rsem.nf.test +++ b/tests/star_rsem.nf.test @@ -14,9 +14,9 @@ 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 ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -25,7 +25,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$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() } @@ -46,9 +46,9 @@ 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 ${params.outdir}/ with stable content - def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore') + def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore') assertAll( { assert workflow.success}, { assert snapshot( @@ -57,7 +57,7 @@ nextflow_pipeline { // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions removeNextflowVersion("$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/star_rsem.nf.test.snap b/tests/star_rsem.nf.test.snap index 51411c86c..1793abee7 100644 --- a/tests/star_rsem.nf.test.snap +++ b/tests/star_rsem.nf.test.snap @@ -190,34 +190,35 @@ "multiqc/star_rsem/multiqc_report_data/cutadapt_filtered_reads_plot.txt", "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Counts.txt", "multiqc/star_rsem/multiqc_report_data/cutadapt_trimmed_sequences_plot_3_Obs_Exp.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc-status-check-heatmap.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_adapter_content_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_overrepresented_sequences_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_n_content_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_base_sequence_quality_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Counts.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot-1_Percentages.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Counts.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_gc_content_plot_Percentages.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_per_sequence_quality_scores_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_counts_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw-status-check-heatmap.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_adapter_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_overrepresented_sequences_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_n_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_base_sequence_quality_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_per_sequence_quality_scores_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_counts_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_raw_top_overrepresented_sequences_table.txt", "multiqc/star_rsem/multiqc_report_data/fastqc_sequence_length_distribution_plot.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table-1.txt", - "multiqc/star_rsem/multiqc_report_data/fastqc_top_overrepresented_sequences_table.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed-status-check-heatmap.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_overrepresented_sequences_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_n_content_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_base_sequence_quality_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Counts.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_per_sequence_quality_scores_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_counts_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_sequence_duplication_levels_plot.txt", + "multiqc/star_rsem/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt", "multiqc/star_rsem/multiqc_report_data/junction_saturation_known.txt", "multiqc/star_rsem/multiqc_report_data/junction_saturation_novel.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc.log", "multiqc/star_rsem/multiqc_report_data/multiqc_citations.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_cutadapt.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_data.json", - "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar-section-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_dupradar.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fail_strand_check_table.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_raw.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_fastqc_fastqc_trimmed.txt", @@ -230,23 +231,15 @@ "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_junction_annotation.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_rseqc_read_distribution.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_salmon.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_1.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_2.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_3.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_clustering-plot_4.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_salmon_deseq2_pca-plot.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_1.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_2.txt", + "multiqc/star_rsem/multiqc_report_data/multiqc_sample-relationships_3.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_flagstat.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_idxstats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_samtools_stats.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_software_versions.txt", "multiqc/star_rsem/multiqc_report_data/multiqc_sources.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_1.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_2.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_3.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_clustering-plot_4.txt", - "multiqc/star_rsem/multiqc_report_data/multiqc_star_rsem_deseq2_pca-plot.txt", "multiqc/star_rsem/multiqc_report_data/picard_deduplication.txt", "multiqc/star_rsem/multiqc_report_data/picard_histogram.txt", "multiqc/star_rsem/multiqc_report_data/picard_histogram_1.txt", @@ -286,32 +279,32 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_filtered_reads_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Counts.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/cutadapt_trimmed_sequences_plot_3_Obs_Exp.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar-section-plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/dupradar.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/fail_strand_check_table.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc-status-check-heatmap.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_adapter_content_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_overrepresented_sequences_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_n_content_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_base_sequence_quality_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Counts.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot-1_Percentages.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Counts.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_gc_content_plot_Percentages.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_per_sequence_quality_scores_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-cnt.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-1-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-cnt.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_counts_plot-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw-status-check-heatmap.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_adapter_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_overrepresented_sequences_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_n_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_base_sequence_quality_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_per_sequence_quality_scores_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-cnt.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_counts_plot-pct.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_raw_top_overrepresented_sequences_table.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_sequence_length_distribution_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table-1.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_top_overrepresented_sequences_table.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed-status-check-heatmap.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_overrepresented_sequences_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_n_content_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_base_sequence_quality_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Counts.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_per_sequence_quality_scores_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-cnt.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_counts_plot-pct.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_sequence_duplication_levels_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/fastqc_trimmed_top_overrepresented_sequences_table.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/featurecounts_biotype_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/general_stats_table.pdf", @@ -338,9 +331,8 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_distribution_plot-pct.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/rseqc_read_dups_plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_clustering-plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_deseq2_pca-plot.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/salmon_plot.pdf", + "multiqc/star_rsem/multiqc_report_plots/pdf/sample-relationships.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Percentage_of_total.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-flagstat-dp_Read_counts.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.pdf", @@ -352,39 +344,37 @@ "multiqc/star_rsem/multiqc_report_plots/pdf/samtools-stats-dp.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-cnt.pdf", "multiqc/star_rsem/multiqc_report_plots/pdf/samtools_alignment_plot-pct.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_clustering-plot.pdf", - "multiqc/star_rsem/multiqc_report_plots/pdf/star_rsem_deseq2_pca-plot.pdf", "multiqc/star_rsem/multiqc_report_plots/png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_filtered_reads_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Counts.png", "multiqc/star_rsem/multiqc_report_plots/png/cutadapt_trimmed_sequences_plot_3_Obs_Exp.png", - "multiqc/star_rsem/multiqc_report_plots/png/dupradar-section-plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/dupradar.png", "multiqc/star_rsem/multiqc_report_plots/png/fail_strand_check_table.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc-status-check-heatmap.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_adapter_content_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_overrepresented_sequences_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_n_content_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_base_sequence_quality_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Counts.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot-1_Percentages.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Counts.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_gc_content_plot_Percentages.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_per_sequence_quality_scores_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-cnt.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-1-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-cnt.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_counts_plot-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw-status-check-heatmap.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_adapter_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_overrepresented_sequences_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_n_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_base_sequence_quality_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_per_sequence_quality_scores_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-cnt.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_counts_plot-pct.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_raw_top_overrepresented_sequences_table.png", "multiqc/star_rsem/multiqc_report_plots/png/fastqc_sequence_length_distribution_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table-1.png", - "multiqc/star_rsem/multiqc_report_plots/png/fastqc_top_overrepresented_sequences_table.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed-status-check-heatmap.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_overrepresented_sequences_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_n_content_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_base_sequence_quality_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Counts.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_per_sequence_quality_scores_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-cnt.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_counts_plot-pct.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_sequence_duplication_levels_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/fastqc_trimmed_top_overrepresented_sequences_table.png", "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/featurecounts_biotype_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/general_stats_table.png", @@ -411,9 +401,8 @@ "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_distribution_plot-pct.png", "multiqc/star_rsem/multiqc_report_plots/png/rseqc_read_dups_plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_clustering-plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/salmon_deseq2_pca-plot.png", "multiqc/star_rsem/multiqc_report_plots/png/salmon_plot.png", + "multiqc/star_rsem/multiqc_report_plots/png/sample-relationships.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Percentage_of_total.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-flagstat-dp_Read_counts.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.png", @@ -425,39 +414,37 @@ "multiqc/star_rsem/multiqc_report_plots/png/samtools-stats-dp.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-cnt.png", "multiqc/star_rsem/multiqc_report_plots/png/samtools_alignment_plot-pct.png", - "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_clustering-plot.png", - "multiqc/star_rsem/multiqc_report_plots/png/star_rsem_deseq2_pca-plot.png", "multiqc/star_rsem/multiqc_report_plots/svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_filtered_reads_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Counts.svg", "multiqc/star_rsem/multiqc_report_plots/svg/cutadapt_trimmed_sequences_plot_3_Obs_Exp.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/dupradar-section-plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/dupradar.svg", "multiqc/star_rsem/multiqc_report_plots/svg/fail_strand_check_table.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc-status-check-heatmap.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_adapter_content_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_overrepresented_sequences_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_n_content_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_base_sequence_quality_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Counts.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot-1_Percentages.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Counts.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_gc_content_plot_Percentages.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_per_sequence_quality_scores_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-cnt.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-1-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-cnt.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_counts_plot-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw-status-check-heatmap.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_adapter_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_overrepresented_sequences_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_n_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_base_sequence_quality_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_per_sequence_quality_scores_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-cnt.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_counts_plot-pct.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_raw_top_overrepresented_sequences_table.svg", "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_sequence_length_distribution_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table-1.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_top_overrepresented_sequences_table.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed-status-check-heatmap.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_overrepresented_sequences_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_n_content_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_base_sequence_quality_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Counts.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_gc_content_plot_Percentages.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_per_sequence_quality_scores_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-cnt.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_counts_plot-pct.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_sequence_duplication_levels_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/fastqc_trimmed_top_overrepresented_sequences_table.svg", "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/featurecounts_biotype_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/general_stats_table.svg", @@ -484,9 +471,8 @@ "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_distribution_plot-pct.svg", "multiqc/star_rsem/multiqc_report_plots/svg/rseqc_read_dups_plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_clustering-plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/salmon_deseq2_pca-plot.svg", "multiqc/star_rsem/multiqc_report_plots/svg/salmon_plot.svg", + "multiqc/star_rsem/multiqc_report_plots/svg/sample-relationships.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Percentage_of_total.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-flagstat-dp_Read_counts.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools-idxstats-mapped-reads-plot_Normalised_Counts-cnt.svg", @@ -498,8 +484,6 @@ "multiqc/star_rsem/multiqc_report_plots/svg/samtools-stats-dp.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-cnt.svg", "multiqc/star_rsem/multiqc_report_plots/svg/samtools_alignment_plot-pct.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_clustering-plot.svg", - "multiqc/star_rsem/multiqc_report_plots/svg/star_rsem_deseq2_pca-plot.svg", "pipeline_info", "pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "salmon", @@ -1139,80 +1123,46 @@ [ "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_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:md5,5a68f7972ea275b21b12acdf43447dfb", "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:md5,27bb37d346e8f0960c882a3676e219e8", "multiqc_samtools_idxstats.txt:md5,1cbc64fc9713831a6f45effc0cfe6a39", - "multiqc_star_rsem_deseq2_pca-plot.txt:md5,7a428c83a9dec1f43ecd4fbbea664ece", "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_multimapping_rates.txt:md5,05878dd307fa1666dd4cc1888de6257a", "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", - 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"timestamp": "2024-10-02T08:31:03.022387" + "timestamp": "2024-10-10T12:45:00.993602" }, "Params: --aligner star_rsem - stub": { "content": [ @@ -1490,13 +1355,14 @@ ], [ "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": "2024-10-02T08:31:54.433237" + "timestamp": "2024-10-10T11:41:09.240442" } -} +} \ No newline at end of file