update snapshot

Author: SusiJo

tests/default.nf.test

@@ -87,7 +87,6 @@ nextflow_pipeline {
                     // Number of successful tasks
                     workflow.trace.succeeded().size(),
                     // pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
-                    removeNextflowVersion("$outputDir/pipeline_info/collated_versions.yml"),
                     removeNextflowVersion("$outputDir/pipeline_info/nf_core_differentialabundance_software_versions.yml"),
                     // All stable path name, with a relative path
                     stable_name,

tests/default.nf.test.snap

@@ -190,7 +190,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-17T15:12:35.519718769"
+        "timestamp": "2025-06-23T09:03:01.551039804"
     },
     "Test profile - with toolsheet": {
         "content": [
@@ -383,7 +383,7 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-17T15:11:12.568576871"
+        "timestamp": "2025-06-23T09:01:41.694097903"
     },
     "Test profile - yml no formula": {
         "content": [
@@ -437,55 +437,6 @@
                     "nf-core/differentialabundance": "v1.6.0dev"
                 }
             },
-            {
-                "CUSTOM_FILTERDIFFERENTIALTABLE": {
-                    "pandas": "1.5.2"
-                },
-                "CUSTOM_TABULARTOGSEACHIP": {
-                    "gawk": "5.1.0"
-                },
-                "CUSTOM_TABULARTOGSEACLS": {
-                    "awk": "1.3.4"
-                },
-                "CUSTOM_TABULARTOGSEAGCT": {
-                    "awk": "1.3.4"
-                },
-                "DESEQ2_DIFFERENTIAL": {
-                    "r-base": "4.1.3",
-                    "bioconductor-deseq2": "1.34.0"
-                },
-                "DESEQ2_NORM": {
-                    "r-base": "4.1.3",
-                    "bioconductor-deseq2": "1.34.0"
-                },
-                "GSEA_GSEA": {
-                    "gsea": "4.3.2"
-                },
-                "GTF_TO_TABLE": {
-                    "atlas-gene-annotation-manipulation": "1.1.1"
-                },
-                "GUNZIP_GTF": {
-                    "gunzip": 1.1
-                },
-                "IMMUNEDECONV": {
-                    "r-immunedeconv": "2.1.0"
-                },
-                "PLOT_DIFFERENTIAL": {
-                    "r-shinyngs": "2.2.4"
-                },
-                "PLOT_EXPLORATORY": {
-                    "r-shinyngs": "2.2.4"
-                },
-                "SHINYNGS_APP": {
-                    "r-shinyngs": "2.2.4"
-                },
-                "VALIDATOR": {
-                    "r-shinyngs": "2.2.4"
-                },
-                "Workflow": {
-                    "nf-core/differentialabundance": "v1.6.0dev"
-                }
-            },
             [
                 "other",
                 "other/deseq2",
@@ -625,6 +576,6 @@
             "nf-test": "0.9.2",
             "nextflow": "25.04.3"
         },
-        "timestamp": "2025-06-16T14:53:08.294104544"
+        "timestamp": "2025-06-23T09:04:21.203865649"
     }
 }