update min_mapped_reads snapshots

Author: maxulysse

tests/.nftignore

@@ -4,42 +4,42 @@ kallisto/*/abundance.{h5,tsv}
 kallisto/*/kallisto_quant.log
 kallisto/*/run_info.json
 kallisto/kallisto.*
-multiqc/**/multiqc_report.html
-multiqc/**/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
-multiqc/**/multiqc_report_data/junction_saturation_known.txt
-multiqc/**/multiqc_report_data/junction_saturation_novel.txt
-multiqc/**/multiqc_report_data/kallisto_alignment.txt
-multiqc/**/multiqc_report_data/multiqc.log
-multiqc/**/multiqc_report_data/multiqc_data.json
-multiqc/**/multiqc_report_data/multiqc_dupradar.txt
-multiqc/**/multiqc_report_data/multiqc_fail_strand_check_table.txt
-multiqc/**/multiqc_report_data/multiqc_general_stats.txt
-multiqc/**/multiqc_report_data/multiqc_kallisto.txt
-multiqc/**/multiqc_report_data/multiqc_picard_dups.txt
-multiqc/**/multiqc_report_data/multiqc_rseqc_bam_stat.txt
-multiqc/**/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
-multiqc/**/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
-multiqc/**/multiqc_report_data/multiqc_rseqc_read_distribution.txt
-multiqc/**/multiqc_report_data/multiqc_salmon.txt
-multiqc/**/multiqc_report_data/multiqc_sample-relationships*.txt
-multiqc/**/multiqc_report_data/multiqc_samtools_{flagstat,stats}.txt
-multiqc/**/multiqc_report_data/multiqc_software_versions.txt
-multiqc/**/multiqc_report_data/multiqc_sources.txt
-multiqc/**/multiqc_report_data/multiqc_star.txt
-multiqc/**/multiqc_report_data/picard_deduplication.txt
-multiqc/**/multiqc_report_data/qualimap_genomic_origin.txt
-multiqc/**/multiqc_report_data/qualimap_rnaseq_genome_results.txt
-multiqc/**/multiqc_report_data/rseqc_bam_stat.txt
-multiqc/**/multiqc_report_data/rseqc_inner_distance*.txt
-multiqc/**/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
-multiqc/**/multiqc_report_data/rseqc_read_*.txt
-multiqc/**/multiqc_report_data/salmon_plot.txt
-multiqc/**/multiqc_report_data/samtools-flagstat-dp_*.txt
-multiqc/**/multiqc_report_data/samtools-stats-dp.txt
-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,multiqc/**}/multiqc_report.html
+{multiqc,multiqc/**}/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.txt
+{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_known.txt
+{multiqc,multiqc/**}/multiqc_report_data/junction_saturation_novel.txt
+{multiqc,multiqc/**}/multiqc_report_data/kallisto_alignment.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc.log
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_data.json
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_dupradar.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_fail_strand_check_table.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_rseqc_bam_stat.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_infer_experiment.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_junction_annotation.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_rseqc_read_distribution.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_salmon.txt
+{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_sources.txt
+{multiqc,multiqc/**}/multiqc_report_data/multiqc_star.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/rseqc_bam_stat.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_inner_distance*.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_junction_{annotation,saturation}_*.txt
+{multiqc,multiqc/**}/multiqc_report_data/rseqc_read_*.txt
+{multiqc,multiqc/**}/multiqc_report_data/salmon_plot.txt
+{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/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

tests/min_mapped_reads.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() }