diff --git a/modules/nf-core/vg/construct/environment.yml b/modules/nf-core/vg/construct/environment.yml
index 27512b7d11a5..715867c37140 100644
--- 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
index 6d31c35b4cb5..036e7b8a8f98 100644
--- 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
index 57ae367d0163..8d17609c8c85 100644
--- 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
index aa58aefab580..6cd69859241f 100644
--- 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
index 007918591be2..ba2cb713ab93 100644
--- a/modules/nf-core/vg/construct/tests/main.nf.test.snap
+++ b/modules/nf-core/vg/construct/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "test-vg-construct-insertions-fasta-vcf-stub": {
         "content": [
             {
-                "0": [
+                "graph": [
                     [
                         {
                             "id": "test"
@@ -10,98 +10,77 @@
                         "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"
@@ -109,26 +88,19 @@
                         "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"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/vg/deconstruct/environment.yml b/modules/nf-core/vg/deconstruct/environment.yml
index d848baba9ae4..715867c37140 100644
--- 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
index 1afd0a23f9d0..a2a62b97b275 100644
--- 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
     """
 }
diff --git a/modules/nf-core/vg/deconstruct/meta.yml b/modules/nf-core/vg/deconstruct/meta.yml
index b31e9161100a..a96ab41f11f3 100644
--- a/modules/nf-core/vg/deconstruct/meta.yml
+++ b/modules/nf-core/vg/deconstruct/meta.yml
@@ -1,6 +1,6 @@
 name: vg_deconstruct
-description: Deconstruct snarls present in a variation graph in GFA format to variants
-  in VCF format
+description: Deconstruct snarls present in a variation graph in GFA format to
+  variants in VCF format
 keywords:
   - vcf
   - gfa
@@ -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:
@@ -28,17 +29,17 @@ input:
         description: Variation graph in GFA format
         pattern: "*.{gfa}"
         ontologies:
-          - edam: http://edamontology.org/format_3975 # GFA 1
+          - edam: http://edamontology.org/format_3975
   - pb:
       type: file
-      description: Optional snarls file (from vg snarls) to avoid recomputing. Usually
-        ends with "pb". See "vg snarls".
+      description: Optional snarls file (from vg snarls) to avoid recomputing.
+        Usually ends with "pb". See "vg snarls".
       pattern: "*.{pb}"
       ontologies: []
   - gbwt:
       type: file
-      description: Optional GBWT file (from vg gbwt) so to only consider alt traversals
-        that correspond to GBWT threads FILE.
+      description: Optional GBWT file (from vg gbwt) so to only consider alt
+        traversals that correspond to GBWT threads FILE.
       pattern: "*.{gbwt}"
       ontologies: []
 output:
@@ -53,13 +54,27 @@ output:
           description: Variants in VCF format
           pattern: "*.{vcf}"
           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:
   - "@heuermh, @subwaystation"
 maintainers:
diff --git a/modules/nf-core/vg/deconstruct/tests/main.nf.test b/modules/nf-core/vg/deconstruct/tests/main.nf.test
index 6b73a48fc970..fee709591c57 100644
--- a/modules/nf-core/vg/deconstruct/tests/main.nf.test
+++ b/modules/nf-core/vg/deconstruct/tests/main.nf.test
@@ -32,11 +32,35 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
 					path(process.out.vcf[0][1]).vcf.summary,
-					process.out.versions
+					sanitizeOutput(process.out, unstableKeys: ['versions_vg'])
 					).match()
 				}
             )
         }
     }
 
+    test("test-vg-deconstruct-stub") {
+        options '-stub'
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ], // meta map
+				    [ file(params.modules_testdata_base_path + 'pangenomics/homo_sapiens/pangenome.gfaffix.gfa', checkIfExists: true) ]
+				]
+				input[1] = []
+                input[2] = []
+
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
+            )
+        }
+    }
+
 }
diff --git a/modules/nf-core/vg/deconstruct/tests/main.nf.test.snap b/modules/nf-core/vg/deconstruct/tests/main.nf.test.snap
index f87af62c52a1..c3d096e3d26b 100644
--- a/modules/nf-core/vg/deconstruct/tests/main.nf.test.snap
+++ b/modules/nf-core/vg/deconstruct/tests/main.nf.test.snap
@@ -2,14 +2,54 @@
     "test-vg-deconstruct": {
         "content": [
             "VcfFile [chromosomes=[], sampleCount=12, variantCount=0, phased=true, phasedAutodetect=true]",
-            [
-                "versions.yml:md5,62f9577d24c55d8d2d4889eac8388c1d"
-            ]
+            {
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,ed8d60911e6163dcb339ba9b2855f155"
+                    ]
+                ],
+                "versions_vg": [
+                    [
+                        "VG_DECONSTRUCT",
+                        "vg",
+                        "1.73.0"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-06-13T09:06:17.888905509",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-28T15:40:45.575458"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
+    },
+    "test-vg-deconstruct-stub": {
+        "content": [
+            {
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_vg": [
+                    [
+                        "VG_DECONSTRUCT",
+                        "vg",
+                        "1.73.0"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-06-13T09:06:24.162512036",
+        "meta": {
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/vg/index/environment.yml b/modules/nf-core/vg/index/environment.yml
index 27512b7d11a5..715867c37140 100644
--- a/modules/nf-core/vg/index/environment.yml
+++ b/modules/nf-core/vg/index/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/index/main.nf b/modules/nf-core/vg/index/main.nf
index fae04ad7d9d7..01b45690a049 100644
--- a/modules/nf-core/vg/index/main.nf
+++ b/modules/nf-core/vg/index/main.nf
@@ -4,8 +4,8 @@ process VG_INDEX {
 
     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)
@@ -13,7 +13,7 @@ process VG_INDEX {
     output:
     tuple val(meta), path("*.xg")       , emit: xg
     tuple val(meta), path("*.vgi")      , emit: vg_index, optional: true
-    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
@@ -27,11 +27,6 @@ process VG_INDEX {
         --threads ${task.cpus} \\
         --xg-name ${prefix}.xg \\
         ${input}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vg: \$(echo \$(vg 2>&1 | head -n 1 | sed 's/vg: variation graph tool, version v//;s/ ".*"//' ))
-    END_VERSIONS
     """
 
     stub:
@@ -43,10 +38,5 @@ process VG_INDEX {
     """
     touch ${prefix}.xg
     ${vg_index}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${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/index/meta.yml b/modules/nf-core/vg/index/meta.yml
index f5479c7eded6..78236188367a 100644
--- a/modules/nf-core/vg/index/meta.yml
+++ b/modules/nf-core/vg/index/meta.yml
@@ -12,7 +12,8 @@ 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:
@@ -33,8 +34,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.xg":
           type: file
-          description: File containing a succinct, queryable version of the input graph(s)
-            or read for GCSA or distance indexing
+          description: File containing a succinct, queryable version of the input
+            graph(s) or read for GCSA or distance indexing
           pattern: "*.xg"
           ontologies: []
   vg_index:
@@ -45,17 +46,31 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.vgi":
           type: file
-          description: An index of the graph(s) created when `--index-sorted-vg` is
-            supplied.
+          description: An index of the graph(s) created when `--index-sorted-vg`
+            is supplied.
           pattern: "*.vgi"
           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/index/tests/main.nf.test b/modules/nf-core/vg/index/tests/main.nf.test
index fdec7348fcc5..1a6622fc94ba 100644
--- a/modules/nf-core/vg/index/tests/main.nf.test
+++ b/modules/nf-core/vg/index/tests/main.nf.test
@@ -50,7 +50,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: [])).match() }
             )
         }
     }
@@ -69,7 +69,7 @@ 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/index/tests/main.nf.test.snap b/modules/nf-core/vg/index/tests/main.nf.test.snap
index 38eb46d0a727..56f42e3eaee1 100644
--- a/modules/nf-core/vg/index/tests/main.nf.test.snap
+++ b/modules/nf-core/vg/index/tests/main.nf.test.snap
@@ -2,23 +2,13 @@
     "test-vg-index": {
         "content": [
             {
-                "0": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.xg:md5,4f619672ffe6edb02b406bba610921a0"
+                        "VG_INDEX",
+                        "vg",
+                        "1.73.0"
                     ]
                 ],
-                "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,9aa19c6010a64042bf65a7655c702b01"
-                ],
-                "versions": [
-                    "versions.yml:md5,9aa19c6010a64042bf65a7655c702b01"
-                ],
                 "vg_index": [
                     
                 ],
@@ -32,32 +22,22 @@
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:06:57.534527776",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-02T16:58:38.163234"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "test-vg-index-stub": {
         "content": [
             {
-                "0": [
+                "versions_vg": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.xg:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "VG_INDEX",
+                        "vg",
+                        "1.73.0"
                     ]
                 ],
-                "1": [
-                    
-                ],
-                "2": [
-                    "versions.yml:md5,9aa19c6010a64042bf65a7655c702b01"
-                ],
-                "versions": [
-                    "versions.yml:md5,9aa19c6010a64042bf65a7655c702b01"
-                ],
                 "vg_index": [
                     
                 ],
@@ -71,10 +51,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-06-13T09:07:06.84537826",
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-09-02T16:58:52.321727"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
 }
\ No newline at end of file