update nftignore and snapshots for salmon and kallisto

Author: maxulysse

tests/.nftignore

@@ -7,11 +7,21 @@ kallisto/kallisto.*
 multiqc/multiqc_report.html
 multiqc/multiqc_report_data/fastqc_trimmed_top_overrepresented_sequences_table.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_general_stats.txt
 multiqc/multiqc_report_data/multiqc_kallisto.txt
+multiqc/multiqc_report_data/multiqc_salmon.txt
 multiqc/multiqc_report_data/multiqc_software_versions.txt
 multiqc/multiqc_report_data/multiqc_sources.txt
+multiqc/multiqc_report_data/salmon_plot.txt
 multiqc/multiqc_report_plots/{pdf,png,svg}/*.{pdf,png,svg}
 pipeline_info/*.{html,json,txt,yml}
+salmon/*/aux_info/fld.gz
+salmon/*/aux_info/meta_info.json
+salmon/*/libParams/flenDist.txt
+salmon/*/logs/salmon_quant.log
+salmon/*/quant.genes.sf
+salmon/*/quant.sf
+salmon/salmon.*
 trimgalore/*fastq.gz_trimming_report.txt

tests/kallisto.nf.test

@@ -50,9 +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 ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -61,7 +61,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$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() }

tests/kallisto.nf.test.snap

@@ -244,7 +244,6 @@
                 "fastqc_trimmed_per_sequence_quality_scores_plot.txt:md5,0f9834cc19f76dd5c87cf8cba7435a7c",
                 "fastqc_trimmed_sequence_counts_plot.txt:md5,6ae4db60425cae4f78b13c798ad1dcf3",
                 "fastqc_trimmed_sequence_duplication_levels_plot.txt:md5,c73407d55fc532e864fa1dc8dbc12874",
-                "multiqc.log:md5,8ad099f7085cbd858f2a8feadd603c71",
                 "multiqc_citations.txt:md5,4cece87a056a29c1338277736855e6ee",
                 "multiqc_cutadapt.txt:md5,aac9581a5670cb55edf564f3d6c1f9a7",
                 "multiqc_fastqc_fastqc_trimmed.txt:md5,26528b0b0d3df6304b80ca8f09619233"

tests/salmon.nf.test

@@ -16,9 +16,9 @@ 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 ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -27,7 +27,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$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() }
@@ -50,9 +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 ${params.outdir}/ with stable content
-            def stable_path = getAllFilesFromDir(params.outdir, false, null, 'tests/.nftignore')
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(
@@ -61,7 +61,7 @@ nextflow_pipeline {
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
                     removeNextflowVersion("$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() }