diff --git a/modules/nf-core/vcf2maf/main.nf b/modules/nf-core/vcf2maf/main.nf
index 2bc4495d248d..8ff1d282fbff 100644
--- a/modules/nf-core/vcf2maf/main.nf
+++ b/modules/nf-core/vcf2maf/main.nf
@@ -16,7 +16,8 @@ process VCF2MAF {
 
     output:
     tuple val(meta), path("*.maf"), emit: maf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('vcf2maf'), val("1.6.22"), emit: versions_vcf2maf, topic: versions
+    tuple val("${task.process}"), val('ensemblvep'), eval('vep --help 2>&1 | sed -n "s/^  ensembl-vep *: //p"'), emit: versions_ensemblvep, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -42,11 +43,6 @@ process VCF2MAF {
         --ref-fasta $fasta \\
         --input-vcf $vcf \\
         --output-maf ${prefix}.maf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vcf2maf: $VERSION\$VEP_VERSION
-    END_VERSIONS
     """
 
     stub:
@@ -60,10 +56,5 @@ process VCF2MAF {
     fi
 
     touch ${prefix}.maf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        vcf2maf: $VERSION\$VEP_VERSION
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/vcf2maf/meta.yml b/modules/nf-core/vcf2maf/meta.yml
index a1a05128b854..02fc6b5fd268 100644
--- a/modules/nf-core/vcf2maf/meta.yml
+++ b/modules/nf-core/vcf2maf/meta.yml
@@ -47,13 +47,46 @@ output:
           description: MAF file produced from VCF
           pattern: "*.maf"
           ontologies: []
+  versions_vcf2maf:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - vcf2maf:
+          type: string
+          description: The name of the tool
+      - "1.6.22":
+          type: string
+          description: The expression to obtain the version of the tool
+  versions_ensemblvep:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - ensemblvep:
+          type: string
+          description: The name of the tool
+      - 'vep --help 2>&1 | sed -n "s/^  ensembl-vep *: //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
+      - vcf2maf:
+          type: string
+          description: The name of the tool
+      - "1.6.22":
+          type: string
+          description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - ensemblvep:
+          type: string
+          description: The name of the tool
+      - 'vep --help 2>&1 | sed -n "s/^  ensembl-vep *: //p"':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@adamrtalbot"
 maintainers:
diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test b/modules/nf-core/vcf2maf/tests/main.nf.test
index 472e235e484e..3bbca1566e95 100644
--- a/modules/nf-core/vcf2maf/tests/main.nf.test
+++ b/modules/nf-core/vcf2maf/tests/main.nf.test
@@ -47,8 +47,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     path(process.out.maf[0][1]).readLines()[5..131],
-                    process.out.versions,
-                    path(process.out.versions[0]).readLines()
+                    process.out.findAll { key, val -> key.startsWith('versions') }
                 ).match() },
             )
         }
@@ -78,7 +77,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert path(process.out.maf[0][1]).readLines().size() == 2 }, // no variants, only header lines
-                { assert snapshot(process.out.versions, path(process.out.versions[0]).readLines()).match() }
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith('versions') }).match() }
             )
         }
     }
@@ -103,8 +102,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).readLines()
+                    sanitizeOutput(process.out)
                     ).match()
                 },
             )
@@ -132,8 +130,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out,
-                    path(process.out.versions[0]).readLines()
+                    sanitizeOutput(process.out)
                     ).match()
                 },
             )
diff --git a/modules/nf-core/vcf2maf/tests/main.nf.test.snap b/modules/nf-core/vcf2maf/tests/main.nf.test.snap
index f0062a0e2a2c..427978880fea 100644
--- a/modules/nf-core/vcf2maf/tests/main.nf.test.snap
+++ b/modules/nf-core/vcf2maf/tests/main.nf.test.snap
@@ -2,7 +2,7 @@
     "Run with VEP - stub": {
         "content": [
             {
-                "0": [
+                "maf": [
                     [
                         {
                             "id": "test"
@@ -10,54 +10,57 @@
                         "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
-                ],
-                "maf": [
+                "versions_ensemblvep": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "VCF2MAF",
+                        "ensemblvep",
+                        "113.0"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
+                "versions_vcf2maf": [
+                    [
+                        "VCF2MAF",
+                        "vcf2maf",
+                        "1.6.22"
+                    ]
                 ]
-            },
-            [
-                "\"VCF2MAF\":",
-                "    vcf2maf: 1.6.22",
-                "    ensemblvep: 113.0"
-            ]
+            }
         ],
+        "timestamp": "2026-07-31T16:35:17.149691833",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-11T16:01:35.707312"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "Run with VEP": {
         "content": [
-            [
-                "versions.yml:md5,999ed581957e1a97cf9a483e5cc65d05"
-            ],
-            [
-                "\"VCF2MAF\":",
-                "    vcf2maf: 1.6.22",
-                "    ensemblvep: 113.0"
-            ]
+            {
+                "versions_ensemblvep": [
+                    [
+                        "VCF2MAF",
+                        "ensemblvep",
+                        "113.0"
+                    ]
+                ],
+                "versions_vcf2maf": [
+                    [
+                        "VCF2MAF",
+                        "vcf2maf",
+                        "1.6.22"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-07-31T15:38:16.241168051",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.1"
-        },
-        "timestamp": "2024-12-11T15:50:59.184221"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "Run without VEP - stub": {
         "content": [
             {
-                "0": [
+                "maf": [
                     [
                         {
                             "id": "test"
@@ -65,31 +68,27 @@
                         "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,f3398fb1c4621649331dca91212dac23"
-                ],
-                "maf": [
+                "versions_ensemblvep": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "VCF2MAF",
+                        "ensemblvep",
+                        "113.0"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,f3398fb1c4621649331dca91212dac23"
+                "versions_vcf2maf": [
+                    [
+                        "VCF2MAF",
+                        "vcf2maf",
+                        "1.6.22"
+                    ]
                 ]
-            },
-            [
-                "\"VCF2MAF\":",
-                "    vcf2maf: 1.6.22"
-            ]
+            }
         ],
+        "timestamp": "2026-07-31T16:35:08.154659422",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-11T15:49:39.498519"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     },
     "Run without VEP": {
         "content": [
@@ -222,18 +221,27 @@
                 "Unknown\t0\t.\tGRCh38\tchr22\t4606\t4606\t+\tTargeted_Region\tINS\tT\tT\t<NON_REF>\t\t\tTUMOR\tNORMAL\tT\tT\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tGTC\t.\t.\t\t\t\t\t\t\t\t\t\t4606",
                 "Unknown\t0\t.\tGRCh38\tchr22\t4608\t4608\t+\tTargeted_Region\tINS\tA\tA\t<NON_REF>\t\t\tTUMOR\tNORMAL\tA\tA\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t.\tCAA\t.\t.\t\t\t\t\t\t\t\t\t\t4608"
             ],
-            [
-                "versions.yml:md5,f3398fb1c4621649331dca91212dac23"
-            ],
-            [
-                "\"VCF2MAF\":",
-                "    vcf2maf: 1.6.22"
-            ]
+            {
+                "versions_ensemblvep": [
+                    [
+                        "VCF2MAF",
+                        "ensemblvep",
+                        "113.0"
+                    ]
+                ],
+                "versions_vcf2maf": [
+                    [
+                        "VCF2MAF",
+                        "vcf2maf",
+                        "1.6.22"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-07-31T15:38:06.822105654",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.2"
-        },
-        "timestamp": "2024-12-11T15:52:16.957598"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.0"
+        }
     }
-}
+}
\ No newline at end of file