update last snapshots

Author: maxulysse

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.*

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"
     }
-}
+}

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() }