update skip_trimming snapshots

Author: maxulysse

tests/hisat2.nf.test.snap

@@ -1309,28 +1309,6 @@
                 "lib_format_counts.json:md5,088fd51db07022ffde47033bbd029400",
                 "R_sessionInfo.log:md5,fb0da0d7ad6994ed66a8e68348b19676",
                 "tx2gene.tsv:md5,0e2418a69d2eba45097ebffc2f700bfe"
-            ],
-            [
-                [
-                    "RAP1_IAA_30M_REP1.markdup.sorted.bam",
-                    "4bf1f3b76f3530504adfdb43b2108d8b"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP1.markdup.sorted.bam",
-                    "2296ff6525d6efb9ffa5b3dcc870dd0d"
-                ],
-                [
-                    "RAP1_UNINDUCED_REP2.markdup.sorted.bam",
-                    "799583958cd2ca6ad49be00651a33359"
-                ],
-                [
-                    "WT_REP1.markdup.sorted.bam",
-                    "aea452c12ed0a10dee2f1b004a7dad95"
-                ],
-                [
-                    "WT_REP2.markdup.sorted.bam",
-                    "6c30c16afec17c44cddfcc9eacea5cd2"
-                ]
             ]
         ],
         "meta": {

tests/skip_trimming.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() }