Update haplogrep3 recipe to use topics

modules/nf-core/haplogrep3/classify/main.nf

@@ -11,8 +11,8 @@ process HAPLOGREP3_CLASSIFY {
     tuple val(meta), path(inputfile)
 
     output:
-    tuple val(meta), path("*.txt"), emit: txt
-    path "versions.yml"           , emit: versions
+    tuple val(meta)             , path("*.txt")                                                                           , emit: txt
+    tuple val("${task.process}"), val('haplogrep3'), eval("haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\).*/\\1/p'"), emit: versions_haplogrep3, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,22 +26,12 @@ process HAPLOGREP3_CLASSIFY {
         $args \\
         --in $inputfile \\
         --out ${prefix}.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        haplogrep3: \$(echo \$(haplogrep3 2>&1) | (sed '2!d') | (sed 's/Haplogrep 3 //'))
-    END_VERSIONS
     """
 
 }

modules/nf-core/haplogrep3/classify/meta.yml

@@ -35,13 +35,27 @@ output:
           description: text file with classification information
           pattern: "*.{txt}"
           ontologies: []
+  versions_haplogrep3:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - haplogrep3:
+          type: string
+          description: The tool name
+      - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\':
+          type: string
+          description: The command used to generate the version of the tool
+topics:
   versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - haplogrep3:
+          type: string
+          description: The tool name
+      - haplogrep3 | sed -n 's/.*Haplogrep 3 \\([0-9.]\\+\\':
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@lucpen"
 maintainers:

modules/nf-core/haplogrep3/classify/tests/main.nf.test.snap

@@ -12,7 +12,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                    [
+                        "HAPLOGREP3_CLASSIFY",
+                        "haplogrep3",
+                        "3.2.2"
+                    ]
                 ],
                 "txt": [
                     [
@@ -23,16 +27,20 @@
                         "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                "versions_haplogrep3": [
+                    [
+                        "HAPLOGREP3_CLASSIFY",
+                        "haplogrep3",
+                        "3.2.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-01-28T15:34:35.106097277"
+        "timestamp": "2025-12-08T14:14:20.562672125"
     },
     "test-haplogrep3-classify": {
         "content": [
@@ -47,7 +55,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                    [
+                        "HAPLOGREP3_CLASSIFY",
+                        "haplogrep3",
+                        "3.2.2"
+                    ]
                 ],
                 "txt": [
                     [
@@ -58,15 +70,19 @@
                         "test.txt:md5,fb242df629aa6168371d1d742f0fb179"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,bd62c94d9b52732b89fbd979ded94a60"
+                "versions_haplogrep3": [
+                    [
+                        "HAPLOGREP3_CLASSIFY",
+                        "haplogrep3",
+                        "3.2.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-01-28T15:36:19.954363253"
+        "timestamp": "2025-12-08T14:14:10.117489085"
     }
 }