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

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

@@ -12,7 +12,7 @@ process ABRICATE_SUMMARY {
 
     output:
     tuple val(meta), path("*.txt"), emit: report
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('abricate'), eval("abricate --version | sed 's/^.* //' "), emit: versions_abricate, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,9 +24,5 @@ process ABRICATE_SUMMARY {
         --summary \\
         ${reports} > ${prefix}.txt
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        abricate: \$(echo \$(abricate --version 2>&1) | sed 's/^.*abricate //' )
-    END_VERSIONS
     """
 }

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

@@ -1,5 +1,6 @@
 name: abricate_summary
-description: Screen assemblies for antimicrobial resistance against multiple databases
+description: Screen assemblies for antimicrobial resistance against multiple
+  databases
 keywords:
   - bacteria
   - assembly
@@ -10,7 +11,8 @@ tools:
       homepage: https://github.com/tseemann/abricate
       documentation: https://github.com/tseemann/abricate
       tool_dev_url: https://github.com/tseemann/abricate
-      licence: ["GPL v2"]
+      licence:
+        - "GPL v2"
       identifier: biotools:ABRicate
 input:
   - - meta:
@@ -23,9 +25,9 @@ input:
         description: FASTA, GenBank or EMBL formatted file
         pattern: "*.{fa,fasta,fna,fa.gz,fasta.gz,fna.gz,gbk,gbk.gz,embl,embl.gz}"
         ontologies:
-          - edam: "http://edamontology.org/format_1929" # FASTA
-          - edam: "http://edamontology.org/format_1936" # GenBank
-          - edam: "http://edamontology.org/format_2204" # EMBL format (XML)
+          - edam: "http://edamontology.org/format_1929"
+          - edam: "http://edamontology.org/format_1936"
+          - edam: "http://edamontology.org/format_2204"
 output:
   report:
     - - meta:
@@ -38,15 +40,30 @@ output:
           description: Tab-delimited report of aggregated 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/summary/tests/main.nf.test.snap

@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1fadc3c51127e35186a8f1d4ec21ea07"
+                    [
+                        "ABRICATE_SUMMARY",
+                        "abricate",
+                        "1.0.1"
+                    ]
                 ],
                 "report": [
                     [
@@ -21,11 +25,19 @@
                         "test_summary.txt:md5,a4ec7010e75404ce3a1033f0c4b4a7f9"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,1fadc3c51127e35186a8f1d4ec21ea07"
+                "versions_abricate": [
+                    [
+                        "ABRICATE_SUMMARY",
+                        "abricate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
-        "timestamp": "2023-10-15T10:55:48.065653059"
+        "timestamp": "2026-03-05T13:01:57.186498",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }