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
-    tuple val("${task.process}"), val('abricate'), eval("abricate --version 2>&1 | sed 's/^.*abricate //'"), emit: versions_abricate_summary, topic: versions
+    tuple val("${task.process}"), val('abricate'), eval("abricate --version | sed 's/^.* //' "), emit: versions_abricate, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,5 +23,6 @@ process ABRICATE_SUMMARY {
     abricate \\
         --summary \\
         ${reports} > ${prefix}.txt
+
     """
 }

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

@@ -25,9 +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:
@@ -40,29 +40,30 @@ output:
           description: Tab-delimited report of aggregated results
           pattern: "*.{txt}"
           ontologies:
-            - edam: "http://edamontology.org/format_2330" # Textual format
-  versions_abricate_summary:
+            - edam: "http://edamontology.org/format_2330"
+  versions_abricate:
     - - ${task.process}:
           type: string
-          description: The name of the process
+          description: The process the versions were collected from
       - abricate:
           type: string
-          description: The name of the tool
-      - abricate --version 2>&1 | sed 's/^.*abricate //':
+          description: The tool name
+      - "abricate --version | sed 's/^.* //' ":
           type: eval
           description: The expression to obtain the version of the tool
 topics:
   versions:
     - - ${task.process}:
           type: string
-          description: The name of the process
+          description: The process the versions were collected from
       - abricate:
           type: string
-          description: The name of the tool
-      - abricate --version 2>&1 | sed 's/^.*abricate //':
+          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

@@ -25,7 +25,7 @@
                         "test_summary.txt:md5,a4ec7010e75404ce3a1033f0c4b4a7f9"
                     ]
                 ],
-                "versions_abricate_summary": [
+                "versions_abricate": [
                     [
                         "ABRICATE_SUMMARY",
                         "abricate",
@@ -34,7 +34,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-11T15:03:55.306937542",
+        "timestamp": "2026-03-05T13:01:57.186498",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"