Migrate hmtnote to topic versions

modules/nf-core/hmtnote/annotate/main.nf

@@ -11,35 +11,26 @@ process HMTNOTE_ANNOTATE {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("*_annotated.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${prefix}.vcf"), emit: vcf
+    tuple val("${task.process}"), val("hmtnote"), eval("hmtnote --version | sed 's/^.*hmtnote, version //'"), emit: versions_hmtnote, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
 
     """
     hmtnote \\
         annotate \\
         $vcf \\
-        ${prefix}_annotated.vcf \\
+        ${prefix}.vcf \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
-    END_VERSIONS
     """
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}_annotated.vcf
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        hmtnote: \$(echo \$(hmtnote --version 2>&1) | sed 's/^.*hmtnote, version //; s/Using.*\$//' ))
-    END_VERSIONS
+    touch ${prefix}.vcf
     """
 }

modules/nf-core/hmtnote/annotate/meta.yml

@@ -1,6 +1,6 @@
 name: hmtnote_annotate
-description: Human mitochondrial variants annotation using HmtVar. Contains .plk file
-  with annotation, so can be run offline
+description: Human mitochondrial variants annotation using HmtVar. Contains .plk
+  file with annotation, so can be run offline
 keywords:
   - hmtnote
   - mitochondria
@@ -29,18 +29,32 @@ output:
           type: map
           description: |
             Groovy Map containing sample information
-      - "*_annotated.vcf":
+      - "${prefix}.vcf":
           type: file
           description: annotated vcf
-          pattern: "*_annotated.vcf"
+          pattern: "*.vcf"
           ontologies: []
+  versions_hmtnote:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - hmtnote:
+          type: string
+          description: Name of the tool
+      - "hmtnote --version | sed 's/^.*hmtnote, version //'":
+          type: eval
+          description: The expression to obtain 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: Name of the process
+      - hmtnote:
+          type: string
+          description: Name of the tool
+      - "hmtnote --version | sed 's/^.*hmtnote, version //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@sysbiocoder"
 maintainers:

modules/nf-core/hmtnote/annotate/tests/main.nf.test

@@ -33,7 +33,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.vcf[0][1]).vcf.variantsMD5,
-					process.out.versions
+					process.out.findAll {key, value -> key.startsWith("versions")}
 					).match()
 				}
             )

modules/nf-core/hmtnote/annotate/tests/main.nf.test.snap

@@ -7,42 +7,56 @@
                         {
                             "id": "test"
                         },
-                        "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,8e722884ffb75155212a3fc053918766"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
+                    [
+                        "HMTNOTE_ANNOTATE",
+                        "hmtnote",
+                        "0.7.2"
+                    ]
                 ],
                 "vcf": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_annotated.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.vcf:md5,8e722884ffb75155212a3fc053918766"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
+                "versions_hmtnote": [
+                    [
+                        "HMTNOTE_ANNOTATE",
+                        "hmtnote",
+                        "0.7.2"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-02-16T15:50:52.013649",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-05-15T13:43:56.953856721"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.2"
+        }
     },
     "sarscov2": {
         "content": [
             "98d1056442ec88659f26dfb1251b6f74",
-            [
-                "versions.yml:md5,8ee58af72515ea6d362a7721c3ba1340"
-            ]
+            {
+                "versions_hmtnote": [
+                    [
+                        "HMTNOTE_ANNOTATE",
+                        "hmtnote",
+                        "0.7.2"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-02-16T16:05:54.919448",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.2"
-        },
-        "timestamp": "2025-05-15T13:43:44.674273215"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.2"
+        }
     }
 }