update snapshot pipeline level tests

Author: CaroAMN

tests/default.nf.test

@@ -33,4 +33,34 @@ nextflow_pipeline {
             )
         }
     }
+
+    test("default test gpu -stub") {
+
+        options "-stub"
+        when {
+            params {
+                outdir = "$outputDir"
+            }
+        }
+
+        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 ${params.outdir}/ with stable content
+            def stable_path = getAllFilesFromDir(params.outdir, ignoreFile: 'tests/.nftignore')
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    // Number of successful tasks
+                    workflow.trace.succeeded().size(),
+                    // pipeline versions.yml file for multiqc from which Nextflow version is removed because we test pipelines on multiple Nextflow versions
+                    removeNextflowVersion("$outputDir/pipeline_info/nf_core_lsmquant_software_mqc_versions.yml"),
+                    // All stable path name, with a relative path
+                    stable_name,
+                    // All files with stable contents
+                    stable_path
+                ).match() }
+            )
+        }
+    }
 }

tests/default.nf.test.snap

@@ -1,4 +1,88 @@
 {
+    "default test gpu -stub": {
+        "content": [
+            8,
+            {
+                "MAT2JSON_INT": {
+                    "mat2json": 1.0
+                },
+                "NUMORPH3DUNET": {
+                    "numorph3dunet": 1.0
+                },
+                "NUMORPHALIGN": {
+                    "numorphalign": 1.0
+                },
+                "NUMORPHINTENSITY": {
+                    "numorphintensity": 1.0
+                },
+                "NUMORPHSTITCH": {
+                    "numorphstitch": 1.0
+                },
+                "UNZIP": {
+                    "7za": 16.02
+                },
+                "Workflow": {
+                    "nf-core/lsmquant": "v1.0dev"
+                }
+            },
+            [
+                "mat2json",
+                "mat2json/align",
+                "mat2json/align/TEST1.json",
+                "mat2json/intensity",
+                "mat2json/intensity/TEST1.json",
+                "mat2json/stitch",
+                "mat2json/stitch/TEST1.json",
+                "numorph3dunet",
+                "numorph3dunet/TEST1",
+                "numorph3dunet/TEST1/TEST1.csv",
+                "numorph3dunet/TEST1/TEST1_counts.csv",
+                "numorphalign",
+                "numorphalign/TEST1",
+                "numorphalign/TEST1/samples",
+                "numorphalign/TEST1/samples/alignment",
+                "numorphalign/TEST1/samples/alignment/TEST1_full.tif",
+                "numorphalign/TEST1/variables",
+                "numorphalign/TEST1/variables/alignment_table.mat",
+                "numorphalign/TEST1/variables/path_table.mat",
+                "numorphalign/TEST1/variables/z_displacement_align.mat",
+                "numorphintensity",
+                "numorphintensity/TEST1",
+                "numorphintensity/TEST1/samples",
+                "numorphintensity/TEST1/samples/intensity_adjustment",
+                "numorphintensity/TEST1/samples/intensity_adjustment/TEST1.png",
+                "numorphintensity/TEST1/variables",
+                "numorphintensity/TEST1/variables/adj_params.mat",
+                "numorphintensity/TEST1/variables/path_table.mat",
+                "numorphintensity/TEST1/variables/thresholds.mat",
+                "numorphstitch",
+                "numorphstitch/TEST1",
+                "numorphstitch/TEST1/stitched",
+                "numorphstitch/TEST1/stitched/TEST1_stitched.tif",
+                "numorphstitch/TEST1/variables",
+                "numorphstitch/TEST1/variables/adjusted_z.mat",
+                "numorphstitch/TEST1/variables/path_table.mat",
+                "numorphstitch/TEST1/variables/stitch_tforms.mat",
+                "numorphstitch/TEST1/variables/z_dips_matrix.mat",
+                "pipeline_info",
+                "pipeline_info/nf_core_lsmquant_software_mqc_versions.yml",
+                "unzip",
+                "unzip/TEST1"
+            ],
+            [
+                "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "TEST1.json:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "TEST1_full.tif:md5,d41d8cd98f00b204e9800998ecf8427e",
+                "TEST1_stitched.tif:md5,d41d8cd98f00b204e9800998ecf8427e"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "25.04.6"
+        },
+        "timestamp": "2025-09-01T13:52:09.520222007"
+    },
     "default test gpu": {
         "content": [
             8,