fix(kofamscan): migrate to topic versions and add stub testing

modules/nf-core/kofamscan/main.nf

@@ -15,7 +15,7 @@ process KOFAMSCAN {
     output:
     tuple val(meta), path('*.txt'), optional: true, emit: txt
     tuple val(meta), path('*.tsv'), optional: true, emit: tsv
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('kofamscan'), eval("exec_annotation --version 2>&1 | sed 's/exec_annotation //;'"), topic: versions, emit: versions_kofamscan
 
     when:
     task.ext.when == null || task.ext.when
@@ -33,10 +33,14 @@ process KOFAMSCAN {
         --cpu $task.cpus \\
         -o ${prefix}.${extension} \\
         $fasta
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        kofamscan: \$(echo \$(exec_annotation --version 2>&1) | sed 's/^.*exec_annotation //;')
-    END_VERSIONS
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def extension = args.contains("--format detail-tsv") ? "tsv" :
+                    "txt"
+    """
+    touch ${prefix}.${extension}
     """
 }

modules/nf-core/kofamscan/meta.yml

@@ -1,6 +1,6 @@
 name: "kofamscan"
-description: Produces annotation using kofamscan against a Profile database and a
-  KO list
+description: Produces annotation using kofamscan against a Profile database and
+  a KO list
 keywords:
   - fasta
   - kegg
@@ -13,7 +13,8 @@ tools:
       documentation: "https://github.com/takaram/kofam_scan"
       tool_dev_url: "https://github.com/takaram/kofam_scan"
       doi: "10.1093/bioinformatics/btz859"
-      licence: ["MIT License"]
+      licence:
+        - "MIT License"
       identifier: biotools:kofamscan
 input:
   - - meta:
@@ -38,34 +39,48 @@ input:
 output:
   txt:
     - - meta:
-          type: file
-          description: Application-specific text file with hits information
-          pattern: "*.{txt}"
-          ontologies: []
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*.txt":
           type: file
           description: Application-specific text file with hits information
           pattern: "*.{txt}"
           ontologies: []
   tsv:
     - - meta:
-          type: file
-          description: Application-specific text file with hits information
-          pattern: "*.{txt}"
-          ontologies: []
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
       - "*.tsv":
           type: file
           description: Tab separated file containing with detailed hits
           pattern: "*.{tsv}"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+  versions_kofamscan:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - kofamscan:
+          type: string
+          description: kofamscan version string
+      - "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'":
+          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 name of the process
+      - kofamscan:
+          type: string
+          description: kofamscan version string
+      - "exec_annotation --version 2>&1 | sed 's/exec_annotation //;'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@toniher"
 maintainers:

modules/nf-core/kofamscan/tests/main.nf.test

@@ -50,7 +50,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert process.out.txt },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -93,7 +93,53 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.tsv.get(0).get(1)).exists() },
-                { assert snapshot(process.out.versions).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
+            )
+        }
+    }
+
+    test("test_kofamscan_txt - stub") {
+
+        options "-stub"
+
+        setup {
+            run("UNTAR") {
+                script "../../untar/main.nf"
+
+                process {
+                    """
+                    input[0] = [[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/profiles.tar.gz',checkIfExists:true)]
+                    """
+                }
+            }
+
+            run("GUNZIP") {
+                script "../../gunzip/main.nf"
+
+                process {
+                    """
+                    input[0] = [[],file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kofamscan/ko_list.gz',checkIfExists:true)]
+                    """
+                }
+            }
+        }
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [[id:'test'], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/proteome.fasta',checkIfExists: true)]
+                input[1] = UNTAR.out.untar.map{it[1]}
+                input[2] = GUNZIP.out.gunzip.map{it[1]}
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.txt },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }

modules/nf-core/kofamscan/tests/main.nf.test.snap

@@ -1,26 +1,56 @@
 {
     "test_kofamscan_tsv": {
         "content": [
-            [
-                "versions.yml:md5,27e1b383c38beae2cdebb2cc79ff061e"
-            ]
+            {
+                "versions_kofamscan": [
+                    [
+                        "KOFAMSCAN",
+                        "kofamscan",
+                        "1.3.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-04-30T11:04:48.94643",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2025-03-25T09:10:30.450619346"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "test_kofamscan_txt - stub": {
+        "content": [
+            {
+                "versions_kofamscan": [
+                    [
+                        "KOFAMSCAN",
+                        "kofamscan",
+                        "1.3.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T11:05:05.206627",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test_kofamscan_txt": {
         "content": [
-            [
-                "versions.yml:md5,27e1b383c38beae2cdebb2cc79ff061e"
-            ]
+            {
+                "versions_kofamscan": [
+                    [
+                        "KOFAMSCAN",
+                        "kofamscan",
+                        "1.3.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-04-30T11:04:27.92766",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2025-03-24T13:54:47.35695004"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
-}
+}