diff --git a/modules/nf-core/duphold/main.nf b/modules/nf-core/duphold/main.nf
index 099ebddcebbe..0b0af24275e2 100644
--- a/modules/nf-core/duphold/main.nf
+++ b/modules/nf-core/duphold/main.nf
@@ -14,7 +14,7 @@ process DUPHOLD {
 
     output:
     tuple val(meta), path("*.vcf.gz")   , emit: vcf
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val('duphold'), eval('duphold -h | sed -e "s/^version: //;q"'), emit: versions_duphold, topic: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,21 +34,11 @@ process DUPHOLD {
         --bam ${alignment_file} \\
         --fasta ${fasta} \\
         ${snp_annotation}
-
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
-    END_VERSIONS
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | gzip > ${prefix}.vcf.gz
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        duphold: \$(duphold -h | head -n 1 | sed -e "s/^version: //")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/duphold/meta.yml b/modules/nf-core/duphold/meta.yml
index f9cc63b96262..8a1e9ce41421 100644
--- a/modules/nf-core/duphold/meta.yml
+++ b/modules/nf-core/duphold/meta.yml
@@ -18,8 +18,9 @@ tools:
       documentation: "https://github.com/brentp/duphold"
       tool_dev_url: "https://github.com/brentp/duphold"
       doi: "10.1093/gigascience/giz040"
-      licence: ["MIT"]
-      identifier: ""
+      licence:
+        - "MIT"
+      identifier: biotools:duphold
 input:
   - - meta:
         type: map
@@ -71,13 +72,27 @@ output:
           pattern: "*.vcf.gz"
           ontologies:
             - edam: http://edamontology.org/format_3989 # GZIP format
+  versions_duphold:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - duphold:
+          type: string
+          description: The name of the tool
+      - 'duphold -h | sed -e "s/^version: //;q"':
+          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
+      - duphold:
+          type: string
+          description: The name of the tool
+      - 'duphold -h | sed -e "s/^version: //;q"':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@nvnieuwk"
 maintainers:
diff --git a/modules/nf-core/duphold/tests/main.nf.test b/modules/nf-core/duphold/tests/main.nf.test
index 1d5e019a8084..d1402fa64e5f 100644
--- a/modules/nf-core/duphold/tests/main.nf.test
+++ b/modules/nf-core/duphold/tests/main.nf.test
@@ -30,7 +30,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     process.out.vcf.collect{ [
                         path(it[1]).vcf.summary,
                         path(it[1]).vcf.variantsMD5
@@ -63,7 +63,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     process.out.vcf.collect{ [
                         path(it[1]).vcf.summary,
                         path(it[1]).vcf.variantsMD5
@@ -94,7 +94,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-                    process.out.versions,
+                    process.out.findAll { key, val -> key.startsWith('versions') },
                     process.out.vcf.collect{ [
                         path(it[1]).vcf.summary,
                         path(it[1]).vcf.variantsMD5
diff --git a/modules/nf-core/duphold/tests/main.nf.test.snap b/modules/nf-core/duphold/tests/main.nf.test.snap
index 2be32462be93..46eac887a516 100644
--- a/modules/nf-core/duphold/tests/main.nf.test.snap
+++ b/modules/nf-core/duphold/tests/main.nf.test.snap
@@ -1,9 +1,15 @@
 {
     "homo_sapiens - bam gvcf - fasta": {
         "content": [
-            [
-                "versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
-            ],
+            {
+                "versions_duphold": [
+                    [
+                        "DUPHOLD",
+                        "duphold",
+                        "0.2.1"
+                    ]
+                ]
+            },
             [
                 [
                     "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
@@ -11,17 +17,23 @@
                 ]
             ]
         ],
+        "timestamp": "2026-03-13T11:07:13.139440214",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T12:29:08.458156285"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "homo_sapiens - bam gvcf snp - fasta": {
         "content": [
-            [
-                "versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
-            ],
+            {
+                "versions_duphold": [
+                    [
+                        "DUPHOLD",
+                        "duphold",
+                        "0.2.1"
+                    ]
+                ]
+            },
             [
                 [
                     "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
@@ -29,17 +41,23 @@
                 ]
             ]
         ],
+        "timestamp": "2026-03-13T11:10:11.886968148",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T12:29:24.054557879"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "homo_sapiens - cram gvcf - fasta": {
         "content": [
-            [
-                "versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
-            ],
+            {
+                "versions_duphold": [
+                    [
+                        "DUPHOLD",
+                        "duphold",
+                        "0.2.1"
+                    ]
+                ]
+            },
             [
                 [
                     "VcfFile [chromosomes=[chr22], sampleCount=1, variantCount=130, phased=false, phasedAutodetect=false]",
@@ -47,11 +65,11 @@
                 ]
             ]
         ],
+        "timestamp": "2026-03-13T11:07:20.967522367",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T12:29:16.114897779"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "homo_sapiens - bam gvcf - fasta -- stub": {
         "content": [
@@ -65,7 +83,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
+                    [
+                        "DUPHOLD",
+                        "duphold",
+                        "0.2.1"
+                    ]
                 ],
                 "vcf": [
                     [
@@ -75,22 +97,22 @@
                         "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,4c23c9290dc401d7b056d862f72c95a4"
+                "versions_duphold": [
+                    [
+                        "DUPHOLD",
+                        "duphold",
+                        "0.2.1"
+                    ]
                 ]
             },
             [
-                {
-                    "DUPHOLD": {
-                        "duphold": "0.2.1"
-                    }
-                }
+                
             ]
         ],
+        "timestamp": "2026-03-13T11:04:28.096812722",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
-        },
-        "timestamp": "2025-03-26T09:46:42.503938847"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file