diff --git a/modules/nf-core/genmod/annotate/environment.yml b/modules/nf-core/genmod/annotate/environment.yml
index 304fc525fc4f..ca9e18a0acee 100644
--- a/modules/nf-core/genmod/annotate/environment.yml
+++ b/modules/nf-core/genmod/annotate/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.10.1
+  - bioconda::genmod=3.10.2
diff --git a/modules/nf-core/genmod/annotate/main.nf b/modules/nf-core/genmod/annotate/main.nf
index 1d46a12a51a7..a4d13c649a00 100644
--- a/modules/nf-core/genmod/annotate/main.nf
+++ b/modules/nf-core/genmod/annotate/main.nf
@@ -4,15 +4,15 @@ process GENMOD_ANNOTATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
-        'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
+        'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_annotate.vcf"), emit: vcf
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,21 +26,11 @@ process GENMOD_ANNOTATE {
         $args \\
         --outfile ${prefix}_annotate.vcf \\
         $input_vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_annotate.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/genmod/annotate/meta.yml b/modules/nf-core/genmod/annotate/meta.yml
index 8c090c38b695..65f8fda0cb62 100644
--- a/modules/nf-core/genmod/annotate/meta.yml
+++ b/modules/nf-core/genmod/annotate/meta.yml
@@ -35,13 +35,27 @@ output:
           description: Annotated VCF file
           pattern: "*.{vcf}"
           ontologies: []
+  versions_genmod:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          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: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test b/modules/nf-core/genmod/annotate/tests/main.nf.test
index a4b3fccba92b..7b053b2ee8ca 100644
--- a/modules/nf-core/genmod/annotate/tests/main.nf.test
+++ b/modules/nf-core/genmod/annotate/tests/main.nf.test
@@ -26,9 +26,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
-                    ).match() }
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
index ef53e0fad38b..23618cce2413 100644
--- a/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/annotate/tests/main.nf.test.snap
@@ -1,16 +1,23 @@
 {
     "genmod_annotate": {
         "content": [
-            [
-                "versions.yml:md5,06246c96ae9b676262e12828d29a388b"
-            ],
-            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]",
+            "ec9b1d7d21c9f6c0a6e0dffb56732fc3",
+            {
+                "versions_genmod": [
+                    [
+                        "GENMOD_ANNOTATE",
+                        "genmod",
+                        "3.10.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:17.894083851"
+        "timestamp": "2025-12-22T14:45:39.879885252"
     },
     "genmod_annotate - stub": {
         "content": [
@@ -25,7 +32,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,06246c96ae9b676262e12828d29a388b"
+                    [
+                        "GENMOD_ANNOTATE",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -36,15 +47,19 @@
                         "test_annotate.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,06246c96ae9b676262e12828d29a388b"
+                "versions_genmod": [
+                    [
+                        "GENMOD_ANNOTATE",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:23.09633885"
+        "timestamp": "2025-12-22T14:14:43.571171183"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/compound/environment.yml b/modules/nf-core/genmod/compound/environment.yml
index 304fc525fc4f..ca9e18a0acee 100644
--- a/modules/nf-core/genmod/compound/environment.yml
+++ b/modules/nf-core/genmod/compound/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.10.1
+  - bioconda::genmod=3.10.2
diff --git a/modules/nf-core/genmod/compound/main.nf b/modules/nf-core/genmod/compound/main.nf
index 89241c0829fc..86c600fe9c0a 100644
--- a/modules/nf-core/genmod/compound/main.nf
+++ b/modules/nf-core/genmod/compound/main.nf
@@ -4,15 +4,15 @@ process GENMOD_COMPOUND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
-        'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
+        'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf)
 
     output:
     tuple val(meta), path("*_compound.vcf"), emit: vcf
-    path "versions.yml"                    , emit: versions
+    tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -27,21 +27,11 @@ process GENMOD_COMPOUND {
         --processes ${task.cpus} \\
         --outfile ${prefix}_compound.vcf \\
         $input_vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_compound.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/genmod/compound/meta.yml b/modules/nf-core/genmod/compound/meta.yml
index 1c4d16b69caf..87b33921b003 100644
--- a/modules/nf-core/genmod/compound/meta.yml
+++ b/modules/nf-core/genmod/compound/meta.yml
@@ -35,13 +35,27 @@ output:
           description: Output VCF file
           pattern: "*.{vcf}"
           ontologies: []
+  versions_genmod:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          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: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test b/modules/nf-core/genmod/compound/tests/main.nf.test
index 4c667c173736..7601266000d7 100644
--- a/modules/nf-core/genmod/compound/tests/main.nf.test
+++ b/modules/nf-core/genmod/compound/tests/main.nf.test
@@ -25,9 +25,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
-                    ).match() }
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/compound/tests/main.nf.test.snap b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
index 4c74264599a0..15d10bc067f6 100644
--- a/modules/nf-core/genmod/compound/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/compound/tests/main.nf.test.snap
@@ -1,16 +1,22 @@
 {
     "genmod_compound": {
         "content": [
-            [
-                "versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
-            ],
-            "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]"
+            "VcfFile [chromosomes=[MT], sampleCount=3, variantCount=22, phased=false, phasedAutodetect=false]",
+            {
+                "versions_genmod": [
+                    [
+                        "GENMOD_COMPOUND",
+                        "genmod",
+                        "3.10.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:29.069803275"
+        "timestamp": "2025-12-22T14:47:53.481557902"
     },
     "genmod_compound - stub": {
         "content": [
@@ -25,7 +31,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
+                    [
+                        "GENMOD_COMPOUND",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -36,15 +46,19 @@
                         "test_compound.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,94cc11c1afdb852817e5c933a699076f"
+                "versions_genmod": [
+                    [
+                        "GENMOD_COMPOUND",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:34.388372156"
+        "timestamp": "2025-12-22T14:14:51.229110934"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/models/environment.yml b/modules/nf-core/genmod/models/environment.yml
index 304fc525fc4f..ca9e18a0acee 100644
--- a/modules/nf-core/genmod/models/environment.yml
+++ b/modules/nf-core/genmod/models/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.10.1
+  - bioconda::genmod=3.10.2
diff --git a/modules/nf-core/genmod/models/main.nf b/modules/nf-core/genmod/models/main.nf
index a20d3373ddce..8418a178f200 100644
--- a/modules/nf-core/genmod/models/main.nf
+++ b/modules/nf-core/genmod/models/main.nf
@@ -4,8 +4,8 @@ process GENMOD_MODELS {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
-        'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
+        'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf), path (fam)
@@ -13,7 +13,7 @@ process GENMOD_MODELS {
 
     output:
     tuple val(meta), path("*_models.vcf"), emit: vcf
-    path "versions.yml"                  , emit: versions
+    tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,21 +32,11 @@ process GENMOD_MODELS {
         --processes ${task.cpus} \\
         --outfile ${prefix}_models.vcf \\
         $input_vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_models.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/genmod/models/meta.yml b/modules/nf-core/genmod/models/meta.yml
index 28e94c31c015..5754d011b43c 100644
--- a/modules/nf-core/genmod/models/meta.yml
+++ b/modules/nf-core/genmod/models/meta.yml
@@ -45,13 +45,27 @@ output:
           description: Output VCF file
           pattern: "*.{vcf}"
           ontologies: []
+  versions_genmod:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          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: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test b/modules/nf-core/genmod/models/tests/main.nf.test
index 0b9a3ebd0115..83fbd40937b8 100644
--- a/modules/nf-core/genmod/models/tests/main.nf.test
+++ b/modules/nf-core/genmod/models/tests/main.nf.test
@@ -27,9 +27,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
-                    ).match() }
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/models/tests/main.nf.test.snap b/modules/nf-core/genmod/models/tests/main.nf.test.snap
index 55848db4a924..2184f631b1c7 100644
--- a/modules/nf-core/genmod/models/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/models/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,eded01951279d59b81dd8444d33d4e57"
+                    [
+                        "GENMOD_MODELS",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -23,28 +27,38 @@
                         "test_models.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,eded01951279d59b81dd8444d33d4e57"
+                "versions_genmod": [
+                    [
+                        "GENMOD_MODELS",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:45.78200017"
+        "timestamp": "2025-12-22T14:14:58.376387801"
     },
     "genmod_models": {
         "content": [
-            [
-                "versions.yml:md5,eded01951279d59b81dd8444d33d4e57"
-            ],
-            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]",
+            {
+                "versions_genmod": [
+                    [
+                        "GENMOD_MODELS",
+                        "genmod",
+                        "3.10.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:40.473343322"
+        "timestamp": "2025-12-22T14:47:59.960270364"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/genmod/score/environment.yml b/modules/nf-core/genmod/score/environment.yml
index 304fc525fc4f..ca9e18a0acee 100644
--- a/modules/nf-core/genmod/score/environment.yml
+++ b/modules/nf-core/genmod/score/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::genmod=3.10.1
+  - bioconda::genmod=3.10.2
diff --git a/modules/nf-core/genmod/score/main.nf b/modules/nf-core/genmod/score/main.nf
index 8d318c2ef659..fa4ac0795a6e 100644
--- a/modules/nf-core/genmod/score/main.nf
+++ b/modules/nf-core/genmod/score/main.nf
@@ -4,8 +4,8 @@ process GENMOD_SCORE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genmod:3.10.1--pyh7e72e81_0':
-        'biocontainers/genmod:3.10.1--pyh7e72e81_0' }"
+        'https://depot.galaxyproject.org/singularity/genmod:3.10.2--pyh7e72e81_0':
+        'biocontainers/genmod:3.10.2--pyh7e72e81_0' }"
 
     input:
     tuple val(meta), path(input_vcf), path (fam)
@@ -13,7 +13,7 @@ process GENMOD_SCORE {
 
     output:
     tuple val(meta), path("*_score.vcf"), emit: vcf
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('genmod'), eval("genmod --version | sed 's/^.*genmod version: //'"), emit: versions_genmod, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -31,21 +31,11 @@ process GENMOD_SCORE {
         $config_file \\
         --outfile ${prefix}_score.vcf \\
         $input_vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}_score.vcf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        genmod: \$(echo \$(genmod --version 2>&1) | sed 's/^.*genmod version: //' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/genmod/score/meta.yml b/modules/nf-core/genmod/score/meta.yml
index c3b16291317d..893b620d6a0c 100644
--- a/modules/nf-core/genmod/score/meta.yml
+++ b/modules/nf-core/genmod/score/meta.yml
@@ -44,13 +44,27 @@ output:
           description: Output VCF file
           pattern: "*.{vcf}"
           ontologies: []
+  versions_genmod:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          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: Name of the process
+      - genmod:
+          type: string
+          description: Name of the tool
+      - "genmod --version | sed 's/^.*genmod version: //'":
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@ramprasadn"
 maintainers:
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test b/modules/nf-core/genmod/score/tests/main.nf.test
index 6181f63aeac2..710176292b9b 100644
--- a/modules/nf-core/genmod/score/tests/main.nf.test
+++ b/modules/nf-core/genmod/score/tests/main.nf.test
@@ -27,9 +27,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
                     path(process.out.vcf.get(0).get(1)).vcf.summary,
-                    ).match() }
+                    path(process.out.vcf.get(0).get(1)).vcf.variantsMD5,
+                    process.out.findAll { key, val -> key.startsWith("versions") },
+                ).match() }
             )
         }
 
diff --git a/modules/nf-core/genmod/score/tests/main.nf.test.snap b/modules/nf-core/genmod/score/tests/main.nf.test.snap
index 1b95778d4ae4..9923b99c4e35 100644
--- a/modules/nf-core/genmod/score/tests/main.nf.test.snap
+++ b/modules/nf-core/genmod/score/tests/main.nf.test.snap
@@ -1,16 +1,23 @@
 {
     "genmod_score": {
         "content": [
-            [
-                "versions.yml:md5,1944b143daa23f4698486227258a0a6c"
-            ],
-            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]"
+            "VcfFile [chromosomes=[1], sampleCount=3, variantCount=57, phased=false, phasedAutodetect=false]",
+            "50a04b1524fe1e21e49ebd9afdd0d91e",
+            {
+                "versions_genmod": [
+                    [
+                        "GENMOD_SCORE",
+                        "genmod",
+                        "3.10.2"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:51.996138287"
+        "timestamp": "2025-12-22T14:46:03.729403607"
     },
     "genmod_score - stub": {
         "content": [
@@ -25,7 +32,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,1944b143daa23f4698486227258a0a6c"
+                    [
+                        "GENMOD_SCORE",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -36,15 +47,19 @@
                         "test_score.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,1944b143daa23f4698486227258a0a6c"
+                "versions_genmod": [
+                    [
+                        "GENMOD_SCORE",
+                        "genmod",
+                        "3.10.2"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.04.2"
         },
-        "timestamp": "2025-04-16T11:25:57.29005446"
+        "timestamp": "2025-12-22T14:08:59.88453697"
     }
 }
\ No newline at end of file