Update to topic pneumocat

modules/nf-core/pneumocat/main.nf

@@ -3,6 +3,7 @@ process PNEUMOCAT {
     tag "$meta.id"
     label 'process_low'
 
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/pneumocat:1.2.1--0':
@@ -14,37 +15,26 @@ process PNEUMOCAT {
     output:
     tuple val(meta), path("*.xml"), emit: xml
     tuple val(meta), path("*.txt"), emit: txt
-    path "versions.yml"           , emit: versions
+    // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
+    tuple val("${task.process}"), val('pneumocat'), val("1.2.1"), topic: versions, emit: versions_pneumocat
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
-    def VERSION = '1.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     PneumoCaT.py \\
         --input_directory ./ \\
-        $args \\
-        --threads $task.cpus \\
+        ${args} \\
+        --threads ${task.cpus} \\
         --output_dir .
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pneumocat: $VERSION
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.2.1' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.results.xml
     touch ${prefix}.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pneumocat: $VERSION
-    END_VERSIONS
     """
 }

modules/nf-core/pneumocat/meta.yml

@@ -1,20 +1,18 @@
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json
 name: "pneumocat"
-description: Determine Streptococcus pneumoniae serotype from Illumina paired-end
-  reads
+description: Determine Streptococcus pneumoniae serotype from Illumina paired-end reads
 keywords:
   - fastq
   - serotype
   - Streptococcus pneumoniae
 tools:
   - "pneumocat":
-      description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach
-        to assign capsular type to S.pneumoniae genomic data (Illumina)"
+      description: "PneumoCaT (Pneumococcal Capsular Typing) uses a two-step step approach to assign capsular type to S.pneumoniae genomic data (Illumina)"
       homepage: "https://github.com/ukhsa-collaboration/PneumoCaT"
       documentation: "https://github.com/ukhsa-collaboration/PneumoCaT"
       tool_dev_url: "https://github.com/ukhsa-collaboration/PneumoCaT"
       doi: "10.7717/peerj.2477"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: ""
 input:
   - - meta:
@@ -51,13 +49,29 @@ output:
           description: A detailed description of the predicted serotype
           pattern: "*.txt"
           ontologies: []
+  versions_pneumocat:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pneumocat:
+          type: string
+          description: The name of the tool
+      - 1.2.1:
+          type: string
+          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
+      - pneumocat:
+          type: string
+          description: The name of the tool
+      - 1.2.1:
+          type: string
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@rpetit3"
 maintainers:

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

@@ -19,10 +19,11 @@ nextflow_process {
             }
             process {
                 """
-                input[0] = [[id:'test'],
+                input[0] = [
+                    [id:'test'],
                     [
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists:true),
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists:true)
                     ]
                 ]
                 """
@@ -31,7 +32,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

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

@@ -2,36 +2,21 @@
     "test_pneumocat -- stub": {
         "content": [
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.results.xml:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "1": [
+                "txt": [
                     [
                         {
                             "id": "test"
                         },
                         "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "2": [
-                    "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf"
-                ],
-                "txt": [
+                "versions_pneumocat": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "PNEUMOCAT",
+                        "pneumocat",
+                        "1.2.1"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,d8d36b1fca1892122c5a186c9e8ce9cf"
-                ],
                 "xml": [
                     [
                         {
@@ -42,10 +27,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-08-06T17:25:13.84265496",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
-        },
-        "timestamp": "2025-05-13T14:11:48.37606449"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }