update nextflow version + pipeline tests

Author: CaroAMN

.github/workflows/nf-test-gpu.yml

@@ -26,7 +26,7 @@ env:
   NXF_SINGULARITY_CACHEDIR: ${{ github.workspace }}/.singularity
   NXF_SINGULARITY_LIBRARYDIR: ${{ github.workspace }}/.singularity
   # renovate: datasource=github-releases depName=nextflow-io/nextflow versioning=semver
-  NXF_VER: "25.10.3"
+  NXF_VER: "25.10.4"
 
 jobs:
   get-shards:
@@ -79,7 +79,7 @@ jobs:
         profile: [docker, singularity]
         shard: ${{ fromJson(needs.get-shards.outputs.shard) }}
         NXF_VER:
-          - "25.10.3"
+          - "25.10.4"
         filters: [pipeline]
 
     steps:

tests/default.nf.test

@@ -28,9 +28,9 @@ nextflow_pipeline {
                                         // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"),
                     // All stable path name, with a relative path
-                    stable_name,
+                    stable_path,
                     // All files with stable contents
-                    stable_path
+                    stable_content
                 ).match() }
             )
         }
@@ -46,10 +46,10 @@ nextflow_pipeline {
         }
 
         then {
-            // stable_name: All files + folders in ${params.outdir}/ with a stable name
-            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, ignoreFile: 'tests/.nftignore')
+            // stable_path: All files + folders in ${params.outdir}/ with a stable path
+            def stable_path = getAllFilesFromDir(params.outdir, relative: true, includeDir: true, ignore: ['pipeline_info/*.{html,json,txt}'])
+            // stable_content: All files in ${params.outdir}/ with stable content
+            def stable_content = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
             assertAll(
                 { assert workflow.success},
                 { assert snapshot(

tests/default.nf.test.snap

@@ -18,9 +18,6 @@
                 "NUMORPH_INTENSITY": {
                     "numorph_intensity": "1.0.0"
                 },
-                "UNZIP": {
-                    "7za": 16.02
-                },
                 "VALIDATE_PARAMETERS": {
                     "numorph_param_validation": "1.0.0"
                 },
@@ -35,7 +32,9 @@
                 "mat2json/preprocessing/TEST1/TEST1.json",
                 "multiqc",
                 "multiqc/multiqc_data",
+                "multiqc/multiqc_data/.stub",
                 "multiqc/multiqc_plots",
+                "multiqc/multiqc_plots/.stub",
                 "multiqc/multiqc_report.html",
                 "numorph3dunet",
                 "numorph3dunet/TEST1",
@@ -75,14 +74,16 @@
             ],
             [
                 "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
+                ".stub:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
                 "params_TEST1_lsmquant.csv:md5,a1edc3a22e8f390e473102d0193a8f1c"
             ]
         ],
-        "timestamp": "2026-04-29T15:18:49.500188714",
+        "timestamp": "2026-06-03T17:44:14.056450705",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         }
     },
     "default test gpu": {
@@ -104,9 +105,6 @@
                 "NUMORPH_INTENSITY": {
                     "numorph_intensity": "1.0.0"
                 },
-                "UNZIP": {
-                    "7za": 16.02
-                },
                 "VALIDATE_PARAMETERS": {
                     "numorph_param_validation": "1.0.0"
                 },
@@ -579,10 +577,10 @@
                 "params_TEST1_lsmquant.csv:md5,a1edc3a22e8f390e473102d0193a8f1c"
             ]
         ],
-        "timestamp": "2026-04-29T15:16:32.417361365",
+        "timestamp": "2026-06-03T17:16:05.583772288",
         "meta": {
             "nf-test": "0.9.4",
-            "nextflow": "25.10.3"
+            "nextflow": "25.10.4"
         }
     }
 }