Skip to content

Commit

Permalink
update nftignore and hisat2 snapshots
Browse files Browse the repository at this point in the history
  • Loading branch information
@maxulysse
maxulysse committed Oct 10, 2024
1 parent e5c8c9d commit 20e5e7d
Show file tree
Hide file tree
Showing 3 changed files with 183 additions and 277 deletions.
39 changes: 21 additions & 18 deletions tests/.nftignore
View file
Original file line number Diff line number Diff line change
Expand Up @@ -40,27 +40,30 @@ multiqc/**/multiqc_report_data/samtools_alignment_plot.txt
multiqc/**/multiqc_report_data/star_alignment_plot.txt
multiqc/**/multiqc_report_data/star_summary_table.txt
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/*.{bam,bam.bai}
star_salmon/bigwig/*.{forward,reverse}.bigWig
star_salmon/dupradar/box_plot/*_duprateExpBoxplot.pdf
star_salmon/dupradar/histogram/*_expressionHist.pdf
star_salmon/dupradar/scatter_plot/*_duprateExpDens.pdf
star_salmon/featurecounts/*.featureCounts.txt.summary
star_salmon/log/*.Log.{final.out,out,progress.out}
star_salmon/picard_metrics/*.MarkDuplicates.metrics.txt
star_salmon/qualimap/*/css/*
star_salmon/qualimap/*/images_qualimapReport/*
star_salmon/qualimap/*/qualimapReport.html
star_salmon/qualimap/*/rnaseq_qc_results.txt
star_salmon/rseqc/bam_stat/*.bam_stat.txt
star_salmon/rseqc/read_distribution/*.read_distribution.txt
star_salmon/rseqc/{inner_distance,junction_annotation,junction_saturation,read_duplication}/{bed,log,pdf,rscript,txt,xls}/*
star_salmon/samtools_stats/*.bam.{flagstat,idxstats,stats}
star_salmon/stringtie/*.ballgown/t_data.ctab
star_salmon/stringtie/*.gene.abundance.txt
star_salmon/stringtie/*.{coverage,transcripts}.gtf
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
Expand Down
18 changes: 11 additions & 7 deletions tests/hisat2.nf.test
View file
Original file line number Diff line number Diff line change
Expand Up @@ -14,9 +14,11 @@ 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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
// bam_files: All bam files
def bam_files = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
assertAll(
{ assert workflow.success},
{ assert snapshot(
Expand All @@ -25,9 +27,11 @@ nextflow_pipeline {
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$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() }
)
}
Expand All @@ -46,9 +50,9 @@ 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 ${params.outdir}/ with stable content
def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
assertAll(
{ assert workflow.success},
{ assert snapshot(
Expand All @@ -57,7 +61,7 @@ nextflow_pipeline {
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$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 Down
Loading

0 comments on commit 20e5e7d

Please sign in to comment.