topics bamstats generalstats (#9278)

* topics bamstats generalstats

* fix version

Author: nvnieuwk

modules/nf-core/bamstats/generalstats/main.nf

@@ -11,7 +11,7 @@ process BAMSTATS_GENERALSTATS {
 
     output:
     tuple val(meta), path("*.json"), emit: json
-    path "versions.yml"            , emit: versions
+    tuple val("${task.process}"), val("bamstats"), eval('bamstats --version | grep "version: " | sed -e s"/version: //"'), topic: versions, emit: versions_bamstats
 
     when:
     task.ext.when == null || task.ext.when
@@ -28,11 +28,6 @@ process BAMSTATS_GENERALSTATS {
         $args \\
         -c $task.cpus \\
         -o ${prefix}.json
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
-    END_VERSIONS
     """
 
     stub:
@@ -41,10 +36,5 @@ process BAMSTATS_GENERALSTATS {
 
     """
     touch ${prefix}.json
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bamstats: \$(echo \$(bamstats --version 2>&1) | sed 's/^.*bamstats == version://; s/Using.*\$//' | sed 's/built.*//' )
-    END_VERSIONS
     """
 }

modules/nf-core/bamstats/generalstats/meta.yml

@@ -38,12 +38,26 @@ output:
           pattern: "*.json"
           ontologies:
             - edam: http://edamontology.org/format_3464 # JSON
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_bamstats:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - bamstats:
+          type: string
+          description: The name of the tool
+      - 'bamstats --version | grep "version: " | sed -e s"/version: //':
+          type: string
+          description: The version of the tool
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@johnoooh"

modules/nf-core/bamstats/generalstats/tests/main.nf.test

@@ -26,7 +26,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.json.get(0)[1]).exists() },
-                { assert snapshot(process.out.versions).match("versions") }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
             )
         }
 
@@ -51,7 +51,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.json.get(0)[1]).exists() },
-                { assert snapshot(process.out.versions).match("versions_stub") }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions")}).match() }
             )
         }
 

modules/nf-core/bamstats/generalstats/tests/main.nf.test.snap

@@ -1,26 +1,38 @@
 {
-    "versions_stub": {
+    "sarscov2 - bam - stub": {
         "content": [
-            [
-                "versions.yml:md5,6d858a3f76d1852b879f15436882c3cf"
-            ]
+            {
+                "versions_bamstats": [
+                    [
+                        "BAMSTATS_GENERALSTATS",
+                        "bamstats",
+                        "0.3.5"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-03-19T16:52:19.198122"
+        "timestamp": "2025-10-28T16:24:09.688030951"
     },
-    "versions": {
+    "sarscov2 - bam": {
         "content": [
-            [
-                "versions.yml:md5,6d858a3f76d1852b879f15436882c3cf"
-            ]
+            {
+                "versions_bamstats": [
+                    [
+                        "BAMSTATS_GENERALSTATS",
+                        "bamstats",
+                        "0.3.5"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.2",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2024-03-19T16:52:07.413799"
+        "timestamp": "2025-10-28T16:24:02.056451549"
     }
 }