chore(modules): migrate abricate/run to new version output format

modules/nf-core/abricate/run/main.nf

@@ -12,9 +12,10 @@ process ABRICATE_RUN {
     path databasedir
 
     output:
-    tuple val(meta), path("*.txt"), emit: report
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*.txt"), emit: report    
+    tuple val("${task.process}"), val('abricate'), eval("abricate --version | sed 's/^.* //' "), emit: versions_abricate, topic: versions
 
+
     when:
     task.ext.when == null || task.ext.when
 
@@ -36,20 +37,12 @@ process ABRICATE_RUN {
         --threads ${task.cpus} \\
         > ${prefix}.txt
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.txt
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
-    END_VERSIONS
     """
 }

modules/nf-core/abricate/run/meta.yml

@@ -1,5 +1,6 @@
 name: abricate_run
-description: Screen assemblies for antimicrobial resistance against multiple databases
+description: Screen assemblies for antimicrobial resistance against multiple
+  databases
 keywords:
   - bacteria
   - assembly
@@ -28,8 +29,8 @@ input:
           - edam: "http://edamontology.org/format_2204" # EMBL format
   - databasedir:
       type: directory
-      description: Optional location of local copy of database files, possibly with
-        custom databases set up with `abricate --setupdb`
+      description: Optional location of local copy of database files, possibly
+        with custom databases set up with `abricate --setupdb`
       pattern: "*/"
 output:
   report:
@@ -43,15 +44,30 @@ output:
           description: Tab-delimited report of results
           pattern: "*.{txt}"
           ontologies:
-            - edam: "http://edamontology.org/format_2330" # Textual format
+            - edam: "http://edamontology.org/format_2330"
+  versions_abricate:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - abricate:
+          type: string
+          description: The tool name
+      - "abricate --version | sed 's/^.* //' ":
+          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: The process the versions were collected from
+      - abricate:
+          type: string
+          description: The tool name
+      - "abricate --version | sed 's/^.* //' ":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@rpetit3"
+  - "@maxcumminsandfred"
 maintainers:
   - "@rpetit3"

modules/nf-core/abricate/run/tests/main.nf.test.snap

@@ -3,6 +3,13 @@
         "content": [
             {
                 "0": [
+                    [
+                        "ABRICATE_RUN",
+                        "abricate",
+                        "1.0.1"
+                    ]
+                ],
+                "1": [
                     [
                         {
                             "id": "test",
@@ -11,9 +18,6 @@
                         "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
-                ],
                 "report": [
                     [
                         {
@@ -23,21 +27,32 @@
                         "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
+                "versions_abricate": [
+                    [
+                        "ABRICATE_RUN",
+                        "abricate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-02-25T20:44:03.314874",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
-        },
-        "timestamp": "2024-06-19T21:06:27.483697023"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.2"
+        }
     },
     "bacteroides_fragilis - genome.fa.gz": {
         "content": [
             {
                 "0": [
+                    [
+                        "ABRICATE_RUN",
+                        "abricate",
+                        "1.0.1"
+                    ]
+                ],
+                "1": [
                     [
                         {
                             "id": "test",
@@ -46,9 +61,6 @@
                         "test.txt:md5,b48f4f5f78982a221038fd9f0a3aa504"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
-                ],
                 "report": [
                     [
                         {
@@ -58,15 +70,19 @@
                         "test.txt:md5,b48f4f5f78982a221038fd9f0a3aa504"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,2204fb00277c287f5f3d82e28964aa03"
+                "versions_abricate": [
+                    [
+                        "ABRICATE_RUN",
+                        "abricate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-02-25T20:43:54.223267",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-05-23T12:30:00.97526706"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.2"
+        }
     }
 }