Update whamg: topic versions, stub block, sanitizeOutput

modules/nf-core/whamg/main.nf

@@ -16,7 +16,7 @@ process WHAMG {
     tuple val(meta), path("*.vcf.gz")       , emit: vcf
     tuple val(meta), path("*.vcf.gz.tbi")   , emit: tbi
     tuple val(meta), path("*.txt")          , emit: graph, optional: true
-    path "versions.yml"                     , emit: versions
+    tuple val("${task.process}"), val('whamg'), eval('whamg 2>&1 | grep Version | sed \'s/^Version: v//; s/-.*$//\''), topic: versions, emit: versions_whamg
 
     when:
     task.ext.when == null || task.ext.when
@@ -36,10 +36,14 @@ process WHAMG {
         | bgzip ${args2} --threads ${task.cpus} --stdout > ${prefix}.vcf.gz
 
         tabix ${args3} ${prefix}.vcf.gz
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        whamg: \$(echo \$(whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*\$//' ))
-    END_VERSIONS
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    echo "" | gzip > ${prefix}.vcf.gz
+    touch ${prefix}.vcf.gz.tbi
     """
 }

modules/nf-core/whamg/meta.yml

@@ -1,7 +1,8 @@
 name: "whamg"
-description: The wham suite consists of two programs, wham and whamg. wham, the original
-  tool, is a very sensitive method with a high false discovery rate. The second program,
-  whamg, is more accurate and better suited for general structural variant (SV) discovery.
+description: The wham suite consists of two programs, wham and whamg. wham, the
+  original tool, is a very sensitive method with a high false discovery rate.
+  The second program, whamg, is more accurate and better suited for general
+  structural variant (SV) discovery.
 keywords:
   - whamg
   - wham
@@ -15,7 +16,8 @@ tools:
       documentation: "https://github.com/zeeev/wham"
       tool_dev_url: "https://github.com/zeeev/wham"
       doi: "10.1371/journal.pcbi.1004572"
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -55,7 +57,7 @@ output:
           description: Compressed VCF file
           pattern: "*.vcf.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3989 # GZIP format
+            - edam: http://edamontology.org/format_3989
   tbi:
     - - meta:
           type: map
@@ -78,13 +80,27 @@ output:
           description: Graph file
           pattern: "*.txt"
           ontologies: []
+  versions_whamg:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - whamg:
+          type: string
+          description: The name of the tool
+      - "whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*$//'":
+          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
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - whamg:
+          type: string
+          description: The name of the tool
+      - "whamg 2>&1 | grep Version | sed 's/^Version: v//; s/-.*$//'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nvnieuwk"
 maintainers:

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

@@ -30,13 +30,34 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(
-					path(process.out.vcf[0][1]).vcf.summary,
-					file(process.out.tbi[0][1]).name,
-					process.out.graph,
-					process.out.versions
-					).match()
-				}
+                { assert snapshot(sanitizeOutput(process.out)).match() }
+            )
+        }
+    }
+
+    test("test-whamg-bam - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+				    [ id:'test' ], // meta map
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+				    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+				]
+				input[1] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+				input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

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

@@ -1,19 +1,76 @@
 {
     "test-whamg-bam": {
         "content": [
-            "VcfFile [chromosomes=[], sampleCount=1, variantCount=0, phased=true, phasedAutodetect=true]",
-            "test.vcf.gz.tbi",
-            [
-
-            ],
-            [
-                "versions.yml:md5,243bed402cdc21ab2fc42a7400399ea9"
-            ]
+            {
+                "graph": [
+
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,4cb176febbc8c26d717a6c6e67b9c905"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,e45326a91ef59ea91ad3fe85f353748c"
+                    ]
+                ],
+                "versions_whamg": [
+                    [
+                        "WHAMG",
+                        "whamg",
+                        "1.7.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-04-30T17:44:50.968503",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-27T11:43:16.953021"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "test-whamg-bam - stub": {
+        "content": [
+            {
+                "graph": [
+
+                ],
+                "tbi": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions_whamg": [
+                    [
+                        "WHAMG",
+                        "whamg",
+                        "1.7.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-04-30T17:44:56.533951",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }