update nftignore and hisat2 snapshots

Author: maxulysse

tests/.nftignore

@@ -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

tests/hisat2.nf.test

@@ -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 ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            // bam_files: All bam files
+            def bam_files  = getAllFilesFromDir(params.outdir, include: ['**/*.bam'])
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -25,9 +27,11 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$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() }
             )
         }
@@ -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 ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -57,7 +61,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$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() }