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update remove_ribo_rna tests
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@maxulysse
maxulysse committed Oct 10, 2024
1 parent 6866c24 commit 0e2fe1a
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Showing 3 changed files with 162 additions and 294 deletions.
51 changes: 27 additions & 24 deletions tests/.nftignore
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Original file line number Diff line number Diff line change
Expand Up @@ -4,6 +4,31 @@ kallisto/*/abundance.{h5,tsv}
kallisto/*/kallisto_quant.log
kallisto/*/run_info.json
kallisto/kallisto.*
multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt
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_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
{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
Expand All @@ -24,6 +49,7 @@ kallisto/kallisto.*
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sample-relationships*.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_software_versions.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sortmerna.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_sources.txt
{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.txt
{multiqc,multiqc/**}/multiqc_report_data/picard_deduplication.txt
Expand All @@ -37,33 +63,10 @@ kallisto/kallisto.*
{multiqc,multiqc/**}/multiqc_report_data/samtools-flagstat-dp_*.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools-stats-dp.txt
{multiqc,multiqc/**}/multiqc_report_data/samtools_alignment_plot.txt
{multiqc,multiqc/**}/multiqc_report_data/sortmerna-detailed-plot.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}
multiqc/hisat2/multiqc_report_data/hisat2_pe_plot.txt
multiqc/hisat2/multiqc_report_data/hisat2_se_plot.txt
multiqc/hisat2/multiqc_report_data/multiqc_hisat2.txt
pipeline_info/*.{html,json,txt,yml}
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
{salmon,star_salmon}/*/aux_info/fld.gz
{salmon,star_salmon}/*/aux_info/meta_info.json
{salmon,star_salmon}/*/libParams/flenDist.txt
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12 changes: 6 additions & 6 deletions tests/remove_ribo_rna.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
Expand All @@ -25,7 +25,7 @@ nextflow_pipeline {
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$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() }
Expand All @@ -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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
Expand All @@ -57,7 +57,7 @@ nextflow_pipeline {
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$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() }
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