nf-core · SPPearce · Jun 13, 2026
diff --git a/modules/nf-core/vg/construct/environment.yml b/modules/nf-core/vg/construct/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::vg=1.45.0
+  - bioconda::vg=1.73.0
diff --git a/modules/nf-core/vg/construct/main.nf b/modules/nf-core/vg/construct/main.nf
@@ -4,8 +4,8 @@ process VG_CONSTRUCT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/vg:1.45.0--h9ee0642_0':
-        'quay.io/biocontainers/vg:1.45.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/vg:1.73.0--h9ee0642_0':
+        'quay.io/biocontainers/vg:1.73.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(input), path(tbis), path(insertions_fasta)
@@ -14,7 +14,7 @@ process VG_CONSTRUCT {
 
     output:
     tuple val(meta), path("*.vg") , emit: graph
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('vg'), eval("vg 2>&1 | sed -n 's/.*version v\\([0-9.]*\\).*/\\1/p'"), topic: versions, emit: versions_vg
 
     when:
     task.ext.when == null || task.ext.when
@@ -38,21 +38,11 @@ process VG_CONSTRUCT {
         ${input_files} \\
         ${insertions} \\
         > ${prefix}.vg
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vg: \$(echo \$(vg 2>&1 | head -n 1 | sed 's/vg: variation graph tool, version v//;s/ ".*"//' ))
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vg
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vg: \$(echo \$(vg 2>&1 | head -n 1 | sed 's/vg: variation graph tool, version v//;s/ ".*"//' ))
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/vg/construct/meta.yml b/modules/nf-core/vg/construct/meta.yml
@@ -1,6 +1,6 @@
 name: "vg_construct"
-description: Constructs a graph from a reference and variant calls or a multiple sequence
-  alignment file
+description: Constructs a graph from a reference and variant calls or a multiple
+  sequence alignment file
 keywords:
   - vg
   - graph
@@ -15,7 +15,8 @@ tools:
         and variant calling methods.
       homepage: https://github.com/vgteam/vg
       documentation: https://github.com/vgteam/vg/wiki
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: ""
 input:
   - - meta:
@@ -34,8 +35,8 @@ input:
         pattern: "*.tbi"
     - insertions_fasta:
         type: file
-        description: A FASTA file containing insertion sequences (referred to in the
-          VCF file(s))
+        description: A FASTA file containing insertion sequences (referred to in
+          the VCF file(s))
         pattern: "*.{fa,fasta,fna}"
         ontologies: []
   - - meta2:
@@ -45,8 +46,8 @@ input:
           e.g. [ id:'test', single_end:false ]
     - fasta:
         type: file
-        description: The reference FASTA file (cannot be used in combination with `msa`,
-          but is required when using `vcfs`)
+        description: The reference FASTA file (cannot be used in combination with
+          `msa`, but is required when using `vcfs`)
         pattern: "*.{fa,fasta,fna}"
         ontologies: []
   - - meta3:
@@ -71,13 +72,27 @@ output:
           description: The constructed graph
           pattern: "*.vg"
           ontologies: []
+  versions_vg:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - vg:
+          type: string
+          description: The name of the tool
+      - vg 2>&1 | sed -n 's/.*version v\([0-9.]*\).*/\1/p':
+          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
+      - vg:
+          type: string
+          description: The name of the tool
+      - vg 2>&1 | sed -n 's/.*version v\([0-9.]*\).*/\1/p':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nvnieuwk"
 maintainers:

diff --git a/modules/nf-core/vg/construct/tests/main.nf.test b/modules/nf-core/vg/construct/tests/main.nf.test
@@ -37,7 +37,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
             )
         }
     }
@@ -63,7 +63,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
             )
         }
     }
@@ -95,7 +95,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
             )
         }
     }
@@ -127,7 +127,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
             )
         }
     }

diff --git a/modules/nf-core/vg/construct/tests/main.nf.test.snap b/modules/nf-core/vg/construct/tests/main.nf.test.snap
@@ -2,133 +2,105 @@
     "test-vg-construct-insertions-fasta-vcf-stub": {
         "content": [
             {
-                "0": [
+                "graph": [
                     [
                         {
                             "id": "test"
                         },
                         "test.vg:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
-                ],
-                "graph": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.vg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "VG_CONSTRUCT",
+                        "vg",
+                        "1.73.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:06:11.213034116",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-30T11:32:27.550644"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test-vg-construct-insertions-fasta-vcf": {
         "content": [
             {
-                "0": [
+                "graph": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vg:md5,57782ed149d3ba8fef2cc112f49f5a37"
+                        "test.vg:md5,faa32812ad54f50985da3a082ee61887"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
-                ],
-                "graph": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.vg:md5,57782ed149d3ba8fef2cc112f49f5a37"
+                        "VG_CONSTRUCT",
+                        "vg",
+                        "1.73.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:06:04.557473372",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-30T11:32:14.964667"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test-vg-construct-vcf": {
         "content": [
             {
-                "0": [
+                "graph": [
                     [
                         {
                             "id": "test"
                         },
-                        "test.vg:md5,57782ed149d3ba8fef2cc112f49f5a37"
+                        "test.vg:md5,faa32812ad54f50985da3a082ee61887"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
-                ],
-                "graph": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.vg:md5,57782ed149d3ba8fef2cc112f49f5a37"
+                        "VG_CONSTRUCT",
+                        "vg",
+                        "1.73.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:05:46.30677193",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-30T11:31:46.999392"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test-vg-construct-msa": {
         "content": [
             {
-                "0": [
+                "graph": [
                     [
                         {
                             "id": "test"
                         },
                         "test.vg:md5,e93a644ebe4858f0f1f13cd37d22c157"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
-                ],
-                "graph": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.vg:md5,e93a644ebe4858f0f1f13cd37d22c157"
+                        "VG_CONSTRUCT",
+                        "vg",
+                        "1.73.0"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,9c0daae7e404b6c57cc9516eeb2df066"
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:05:53.883929733",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-30T11:31:59.359779"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
diff --git a/modules/nf-core/vg/deconstruct/environment.yml b/modules/nf-core/vg/deconstruct/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::vg=1.43.0
+  - bioconda::vg=1.73.0
diff --git a/modules/nf-core/vg/deconstruct/main.nf b/modules/nf-core/vg/deconstruct/main.nf
@@ -4,8 +4,8 @@ process VG_DECONSTRUCT {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine in ['singularity', 'apptainer'] && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/vg:1.43.0--h9ee0642_0' :
-        'quay.io/biocontainers/vg:1.43.0--h9ee0642_0' }"
+        'https://depot.galaxyproject.org/singularity/vg:1.73.0--h9ee0642_0' :
+        'quay.io/biocontainers/vg:1.73.0--h9ee0642_0' }"
 
     input:
     tuple val(meta), path(gfa)
@@ -14,7 +14,7 @@ process VG_DECONSTRUCT {
 
     output:
     tuple val(meta), path("*.vcf"), emit: vcf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('vg'), eval("vg 2>&1 | sed -n 's/.*version v\\([0-9.]*\\).*/\\1/p'"), topic: versions, emit: versions_vg
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,10 +31,11 @@ process VG_DECONSTRUCT {
         $snarls \\
         $gbwt_arg \\
         $gfa > ${prefix}.vcf
+    """
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vg: \$(vg version 2>&1 | grep -o 'vg .*' | cut -f3 -d ' ' | cut -f2 -d 'v')
-    END_VERSIONS
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.vcf
     """
 }