update skip_qc tests

Author: maxulysse

tests/skip_qc.nf.test

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