Migrate ssuissero to topic channel versions and add stub block

modules/nf-core/ssuissero/main.nf

@@ -13,7 +13,8 @@ process SSUISSERO {
 
     output:
     tuple val(meta), path("*.tsv"), emit: tsv
-    path "versions.yml"           , emit: versions
+    // WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
+    tuple val("${task.process}"), val('ssuissero'), val('1.0.1'), emit: versions_ssuissero, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +23,6 @@ process SSUISSERO {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def is_compressed = fasta.getName().endsWith(".gz") ? true : false
     def fasta_name = fasta.getName().replace(".gz", "")
-    def VERSION = '1.0.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     if [ "$is_compressed" == "true" ]; then
         gzip -c -d $fasta > $fasta_name
@@ -34,10 +34,11 @@ process SSUISSERO {
         -s $prefix \\
         -x fasta \\
         -t $task.cpus
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ssuissero: $VERSION
-    END_VERSIONS
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.tsv
     """
 }

modules/nf-core/ssuissero/meta.yml

@@ -10,7 +10,8 @@ tools:
       homepage: https://github.com/jimmyliu1326/SsuisSero
       documentation: https://github.com/jimmyliu1326/SsuisSero
       tool_dev_url: https://github.com/jimmyliu1326/SsuisSero
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -35,14 +36,28 @@ output:
           description: Tab-delimited serotype prediction
           pattern: "*.{tsv}"
           ontologies:
-            - edam: http://edamontology.org/format_3475 # TSV
+            - edam: http://edamontology.org/format_3475
+  versions_ssuissero:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - ssuissero:
+          type: string
+          description: The name of the tool
+      - 1.0.1:
+          type: string
+          description: 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
+      - ssuissero:
+          type: string
+          description: The name of the tool
+      - 1.0.1:
+          type: string
+          description: The version of the tool
 authors:
   - "@rpetit3"
 maintainers:

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

@@ -15,9 +15,9 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-				    [ id:'test', single_end:false ], // meta map
-				    file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
-				]
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
+                ]
 
                 """
             }
@@ -26,7 +26,31 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("test-ssuissero - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/haemophilus_influenzae/genome/genome.fna.gz', checkIfExists: true)
+                ]
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

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

@@ -1,19 +1,34 @@
 {
-    "test-ssuissero": {
+    "test-ssuissero - stub": {
         "content": [
             {
-                "0": [
+                "tsv": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test_serotyping_res.tsv:md5,559dd2ca386eeb58f3975e3204ce9d43"
+                        "test.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757"
-                ],
+                "versions_ssuissero": [
+                    [
+                        "SSUISSERO",
+                        "ssuissero",
+                        "1.0.1"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-29T16:20:03.264528",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
+    },
+    "test-ssuissero": {
+        "content": [
+            {
                 "tsv": [
                     [
                         {
@@ -23,15 +38,19 @@
                         "test_serotyping_res.tsv:md5,559dd2ca386eeb58f3975e3204ce9d43"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,1343a6174c619ccf3c2469b19ab0a757"
+                "versions_ssuissero": [
+                    [
+                        "SSUISSERO",
+                        "ssuissero",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-04-29T16:19:56.700719",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-27T12:14:54.198227"
+            "nf-test": "0.9.5",
+            "nextflow": "25.10.4"
+        }
     }
 }