swap variantbam to topic

modules/nf-core/variantbam/main.nf

@@ -13,35 +13,23 @@ process VARIANTBAM {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('VariantBam'), val('1.4.4a'), emit: versions_variant, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.4.4a' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     variant \\
         $bam \\
         -o ${prefix}.bam \\
         $args
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        variantbam: $VERSION
-    END_VERSIONS
     """
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def VERSION = '1.4.4a' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
     """
     touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        variantbam: $VERSION
-    END_VERSIONS
     """
 }

modules/nf-core/variantbam/meta.yml

@@ -1,5 +1,6 @@
 name: variantbam
-description: Filtering, downsampling and profiling alignments in BAM/CRAM formats
+description: Filtering, downsampling and profiling alignments in BAM/CRAM
+  formats
 keywords:
   - filter
   - bam
@@ -9,13 +10,14 @@ keywords:
   - subsample bam
 tools:
   - variantbam:
-      description: Filtering and profiling of next-generational sequencing data using
-        region-specific rules
+      description: Filtering and profiling of next-generational sequencing data
+        using region-specific rules
       homepage: https://github.com/walaj/VariantBam
       documentation: https://github.com/walaj/VariantBam#table-of-contents
       tool_dev_url: https://github.com/walaj/VariantBam
       doi: 10.1093/bioinformatics/btw111
-      licence: ["Apache-2.0"]
+      licence:
+        - "Apache-2.0"
       identifier: biotools:variantbam
 input:
   - - meta:
@@ -27,7 +29,9 @@ input:
         type: file
         description: BAM/CRAM file
         pattern: "*.{bam,cram}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_2572 # BAM
+          - edam: http://edamontology.org/format_3462 # CRAM
 output:
   bam:
     - - meta:
@@ -39,14 +43,29 @@ output:
           type: file
           description: Filtered or downsampled BAM file
           pattern: "*.{bam}"
-          ontologies: []
+          ontologies:
+            - edam: http://edamontology.org/format_2572 # BAM
+  versions_variant:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - VariantBam:
+          type: string
+          description: The name of the tool
+      - 1.4.4a:
+          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
+      - VariantBam:
+          type: string
+          description: The name of the tool
+      - 1.4.4a:
+          type: string
+          description: The expression to obtain the version of the tool
 authors:
   - "@bjohnnyd"
 maintainers:

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

@@ -24,7 +24,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
 
             )
         }
@@ -49,7 +49,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
 

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

@@ -2,7 +2,7 @@
     "sarscov2 - bam - stub": {
         "content": [
             {
-                "0": [
+                "bam": [
                     [
                         {
                             "id": "test",
@@ -11,33 +11,25 @@
                         "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,45eda67e09904edc15da264601a307a8"
-                ],
-                "bam": [
+                "versions_variant": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "VARIANTBAM",
+                        "VariantBam",
+                        "1.4.4a"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,45eda67e09904edc15da264601a307a8"
                 ]
             }
         ],
+        "timestamp": "2026-05-21T12:31:49.678638817",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-20T15:10:11.678956173"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "sarscov2 - bam": {
         "content": [
             {
-                "0": [
+                "bam": [
                     [
                         {
                             "id": "test",
@@ -46,27 +38,19 @@
                         "test.bam:md5,fb5b383bb40e3d07cc092e8f97efd5a9"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,45eda67e09904edc15da264601a307a8"
-                ],
-                "bam": [
+                "versions_variant": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,fb5b383bb40e3d07cc092e8f97efd5a9"
+                        "VARIANTBAM",
+                        "VariantBam",
+                        "1.4.4a"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,45eda67e09904edc15da264601a307a8"
                 ]
             }
         ],
+        "timestamp": "2026-05-21T12:31:43.305016973",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-20T15:08:05.260576622"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }