diff --git a/.github/skip_nf_test.json b/.github/skip_nf_test.json
index 9021e031d2b2..baf6b11b059f 100644
--- a/.github/skip_nf_test.json
+++ b/.github/skip_nf_test.json
@@ -72,6 +72,8 @@
         "modules/nf-core/mitohifi/mitohifi",
         "modules/nf-core/molkartgarage/clahe",
         "modules/nf-core/ncbitools/vecscreen",
+        "modules/nf-core/ngscheckmate/fastq",
+        "modules/nf-core/ngscheckmate/vafncm",
         "modules/nf-core/parabricks",
         "modules/nf-core/purgedups/calcuts",
         "modules/nf-core/purgedups/getseqs",
diff --git a/modules/nf-core/ngscheckmate/fastq/main.nf b/modules/nf-core/ngscheckmate/fastq/main.nf
index 8baf32e6e462..70b82ace3265 100644
--- a/modules/nf-core/ngscheckmate/fastq/main.nf
+++ b/modules/nf-core/ngscheckmate/fastq/main.nf
@@ -13,7 +13,7 @@ process NGSCHECKMATE_FASTQ {
 
     output:
     tuple val(meta), path("*.vaf"), emit: vaf
-    path "versions.yml"           , emit: versions
+    tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate
 
     when:
     task.ext.when == null || task.ext.when
@@ -24,23 +24,12 @@ process NGSCHECKMATE_FASTQ {
     def fastq2command  = ( reads instanceof List && reads.size() == 2 ) ? " -2 ${reads[1]} " : ""
 
     """
-    ngscheckmate_fastq  -1 ${reads[0]} $fastq2command ${snp_pt} -p ${task.cpus} $args > ${prefix}.vaf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
+    ngscheckmate_fastq -1 ${reads[0]} $fastq2command ${snp_pt} -p ${task.cpus} $args > ${prefix}.vaf
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.vaf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ngscheckmate/fastq/meta.yml b/modules/nf-core/ngscheckmate/fastq/meta.yml
index cf260469eb8d..be7b9beca064 100644
--- a/modules/nf-core/ngscheckmate/fastq/meta.yml
+++ b/modules/nf-core/ngscheckmate/fastq/meta.yml
@@ -55,13 +55,28 @@ output:
             position contained in the PT file.
           pattern: "*.{vaf}"
           ontologies: []
+  versions_ngscheckmate:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate 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 process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sppearce"
 maintainers:
diff --git a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test
index 5c4dc8037222..673d89f4d206 100644
--- a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test
+++ b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test
@@ -96,8 +96,8 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
@@ -124,9 +124,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap
index 06c3c8b7a80e..f90a32ae4f1b 100644
--- a/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap
+++ b/modules/nf-core/ngscheckmate/fastq/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                    [
+                        "NGSCHECKMATE_FASTQ",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "vaf": [
                     [
@@ -23,16 +27,20 @@
                         "test_paired.vaf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_FASTQ",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-18T09:05:52.332885973"
+        "timestamp": "2025-12-22T08:42:48.87004401"
     },
     "sarscov2 - bam": {
         "content": [
@@ -47,7 +55,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                    [
+                        "NGSCHECKMATE_FASTQ",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "vaf": [
                     [
@@ -58,15 +70,19 @@
                         "test_paired.vaf:md5,a2d18480c8bb7045c39c063faef7e1e4"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9a5d7a8d9148b2ca1ad7d53764ca511a"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_FASTQ",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-18T09:10:36.450684266"
+        "timestamp": "2025-12-23T09:03:49.545360371"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ngscheckmate/ncm/main.nf b/modules/nf-core/ngscheckmate/ncm/main.nf
index 1b5e09aebc95..56e5d18fbab9 100644
--- a/modules/nf-core/ngscheckmate/ncm/main.nf
+++ b/modules/nf-core/ngscheckmate/ncm/main.nf
@@ -17,7 +17,7 @@ process NGSCHECKMATE_NCM {
     tuple val(meta), path("*_all.txt"),         emit: all
     tuple val(meta), path("*.pdf"),             emit: pdf, optional: true
     tuple val(meta), path("*.vcf"),             emit: vcf, optional: true
-    path "versions.yml",                        emit: versions
+    tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,7 +25,7 @@ process NGSCHECKMATE_NCM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def unzip = files.any { it.toString().endsWith(".vcf.gz") }
+    def unzip = files.any {file ->  file.toString().endsWith(".vcf.gz") }
     """
     if ${unzip}
     then
@@ -40,11 +40,6 @@ process NGSCHECKMATE_NCM {
     then
         rm -f *.vcf  # clean up decompressed vcfs
     fi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 
     stub:
@@ -54,10 +49,5 @@ process NGSCHECKMATE_NCM {
     touch ${prefix}_matched.txt
     touch ${prefix}_all.txt
     touch ${prefix}.pdf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ngscheckmate/ncm/meta.yml b/modules/nf-core/ngscheckmate/ncm/meta.yml
index 45fedd04549c..176208e40705 100644
--- a/modules/nf-core/ngscheckmate/ncm/meta.yml
+++ b/modules/nf-core/ngscheckmate/ncm/meta.yml
@@ -106,13 +106,28 @@ output:
             calls used
           pattern: "*.vcf"
           ontologies: []
+  versions_ngscheckmate:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate 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 process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sppearce"
 maintainers:
diff --git a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test
index ce40c2de7ec4..525399ac67e9 100644
--- a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test
+++ b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test
@@ -75,14 +75,15 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(
-                    file(process.out.corr_matrix[0][1]).name, // Content md5 not stable under conda
-                    file(process.out.matched[0][1]).name, // Content md5 not stable under conda
-                    file(process.out.all[0][1]).name, // Content md5 not stable under conda
-                    process.out.versions
-                ).match() }
+                    file(process.out.corr_matrix[0][1]).name,
+                    file(process.out.matched[0][1]).name,
+                    file(process.out.all[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                    ).match()
+                }
             )
         }
 
@@ -106,15 +107,16 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(
                     process.out.corr_matrix,
                     file(process.out.matched[0][1]).name,
                     process.out.all,
                     file(process.out.pdf[0][1]).name,
-                    process.out.versions
-                ).match() }
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                    ).match()
+                }
             )
         }
 
@@ -144,9 +146,10 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match()
+                }
             )
         }
 
@@ -169,9 +172,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test.snap b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test.snap
index 7bf349ed1f67..d9bf7fbdd7b9 100644
--- a/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test.snap
+++ b/modules/nf-core/ngscheckmate/ncm/tests/main.nf.test.snap
@@ -38,7 +38,11 @@
                     
                 ],
                 "5": [
-                    "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "all": [
                     [
@@ -75,8 +79,12 @@
                 "vcf": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
@@ -84,7 +92,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-21T13:57:03.253007571"
+        "timestamp": "2025-12-23T14:05:45.209620774"
     },
     "sarscov2 - vcf": {
         "content": [
@@ -106,30 +114,42 @@
                 ]
             ],
             "test1.pdf",
-            [
-                "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
-            ]
+            {
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-05T15:40:36.013242151"
+        "timestamp": "2025-12-23T09:06:37.902778112"
     },
     "sarscov2 - bam": {
         "content": [
             "combined_bams_output_corr_matrix.txt",
             "combined_bams_matched.txt",
             "combined_bams_all.txt",
-            [
-                "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
-            ]
+            {
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-08-06T11:05:56.136156"
+        "timestamp": "2025-12-21T16:48:41.297586997"
     },
     "sarscov2 - vcf - stub": {
         "content": [
@@ -170,7 +190,11 @@
                     
                 ],
                 "5": [
-                    "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "all": [
                     [
@@ -207,8 +231,12 @@
                 "vcf": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,7ac92d9cbf4fc44b3253832f3a8b2a80"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_NCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
@@ -216,6 +244,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-21T13:57:13.105357464"
+        "timestamp": "2025-12-22T08:41:47.066199532"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ngscheckmate/patterngenerator/main.nf b/modules/nf-core/ngscheckmate/patterngenerator/main.nf
index 02c8a5c1a8a2..2688e43aa360 100644
--- a/modules/nf-core/ngscheckmate/patterngenerator/main.nf
+++ b/modules/nf-core/ngscheckmate/patterngenerator/main.nf
@@ -14,13 +14,12 @@ process NGSCHECKMATE_PATTERNGENERATOR {
 
     output:
     tuple val(meta), path("*.pt"), emit: pt
-    path "versions.yml"          , emit: versions
+    tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
     if ("$fasta" == "${prefix}.fasta") error "makesnvpattern.pl generates a fasta file with the same name as the input fasta, use \"task.ext.prefix\" to disambiguate!"
 
@@ -28,11 +27,6 @@ process NGSCHECKMATE_PATTERNGENERATOR {
     INDEX=\$(find -L ./ -name "*.3.ebwt" | sed 's/\\.3.ebwt\$//')
 
     makesnvpattern.pl ${bed} ${fasta} \$INDEX . ${prefix}
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 
 
@@ -42,10 +36,5 @@ process NGSCHECKMATE_PATTERNGENERATOR {
 
     """
     touch ${prefix}.pt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml
index d65e1ebe6e9a..922758fad9ca 100644
--- a/modules/nf-core/ngscheckmate/patterngenerator/meta.yml
+++ b/modules/nf-core/ngscheckmate/patterngenerator/meta.yml
@@ -61,13 +61,28 @@ output:
             from within raw data
           pattern: "*.pt"
           ontologies: []
+  versions_ngscheckmate:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate 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 process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sppearce"
 maintainers:
diff --git a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test
index cc5fc0d20be1..c1ae851c8bca 100644
--- a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test
+++ b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test
@@ -45,11 +45,13 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert process.out.pt.get(0).get(1).endsWith("test.pt") },
-                { assert snapshot(process.out.versions).match("versions") }
-
+                { assert snapshot(
+                    file(process.out.pt.get(0).get(1)).name,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                    ).match()
+                }
             )
         }
 
@@ -76,9 +78,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test.snap b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test.snap
index ffbcb76514cb..7513247af871 100644
--- a/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test.snap
+++ b/modules/nf-core/ngscheckmate/patterngenerator/tests/main.nf.test.snap
@@ -11,7 +11,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,9a3d382a0bee9591e98740ee777b8262"
+                    [
+                        "NGSCHECKMATE_PATTERNGENERATOR",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "pt": [
                     [
@@ -21,27 +25,38 @@
                         "test.pt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,9a3d382a0bee9591e98740ee777b8262"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_PATTERNGENERATOR",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-18T09:06:32.475789547"
+        "timestamp": "2025-12-22T08:43:45.729357447"
     },
-    "versions": {
+    "sarscov2": {
         "content": [
-            [
-                "versions.yml:md5,9a3d382a0bee9591e98740ee777b8262"
-            ]
+            "test.pt",
+            {
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_PATTERNGENERATOR",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-18T09:11:21.284926012"
+        "timestamp": "2025-12-21T14:49:38.059109225"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/ngscheckmate/vafncm/main.nf b/modules/nf-core/ngscheckmate/vafncm/main.nf
index 47d446c8357e..200c936eb941 100644
--- a/modules/nf-core/ngscheckmate/vafncm/main.nf
+++ b/modules/nf-core/ngscheckmate/vafncm/main.nf
@@ -14,7 +14,7 @@ process NGSCHECKMATE_VAFNCM {
     tuple val(meta), path("*_corr_matrix.txt") , emit: corr_matrix
     tuple val(meta), path("*_all.txt")         , emit: all
     tuple val(meta), path("*_matched.txt")     , emit: matched
-    path "versions.yml"                        , emit: versions
+    tuple val("${task.process}"), val('ngscheckmate'), eval("ncm.py --help | sed '7!d;s/.* v//g'"), topic: versions, emit: versions_ngscheckmate
 
     when:
     task.ext.when == null || task.ext.when
@@ -22,7 +22,6 @@ process NGSCHECKMATE_VAFNCM {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     # tool has a bug where it misses the final file, so add a dummy one.
     cp ${vafs[0]} zzzzzz.vaf
@@ -34,26 +33,14 @@ process NGSCHECKMATE_VAFNCM {
 
     # generate a file with all the samples that do match, for consistency with the bam mode (ngscheckmate/ncm)
     sed "/unmatched/d" ${prefix}_all.txt > ${prefix}_matched.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-
     """
     touch ${prefix}_corr_matrix.txt
     touch ${prefix}_matched.txt
     touch ${prefix}_all.txt
     touch ${prefix}.pdf
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        ngscheckmate: \$(ncm.py --help | sed "7!d;s/ *Ensuring Sample Identity v//g")
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/ngscheckmate/vafncm/meta.yml b/modules/nf-core/ngscheckmate/vafncm/meta.yml
index 53ec285627ca..5538a0df7714 100644
--- a/modules/nf-core/ngscheckmate/vafncm/meta.yml
+++ b/modules/nf-core/ngscheckmate/vafncm/meta.yml
@@ -79,13 +79,28 @@ output:
           description: A txt file containing only the samples that match with each other
           pattern: "*matched.txt"
           ontologies: []
+  versions_ngscheckmate:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate 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 process the versions were collected from
+      - ngscheckmate:
+          type: string
+          description: The tool name
+      - "ncm.py --help | sed '7!d;s/.* v//g'":
+          type: string
+          description: The command used to generate the version of the tool
 authors:
   - "@sppearce"
 maintainers:
diff --git a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test
index 708cc696e41d..a60b5fe01c36 100644
--- a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test
+++ b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test
@@ -124,13 +124,14 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
                 { assert snapshot(
                     process.out.corr_matrix,
                     process.out.matched,
                     process.out.all,
-                    process.out.versions).match() }
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                    ).match() }
             )
         }
 
@@ -149,9 +150,9 @@ nextflow_process {
         }
 
         then {
+            assert process.success
             assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(process.out).match()}
             )
         }
 
diff --git a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test.snap b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test.snap
index 622313070ebe..ad09fd2dbd9d 100644
--- a/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test.snap
+++ b/modules/nf-core/ngscheckmate/vafncm/tests/main.nf.test.snap
@@ -35,7 +35,11 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
+                    [
+                        "NGSCHECKMATE_VAFNCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ],
                 "all": [
                     [
@@ -69,16 +73,20 @@
                         "combined.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_VAFNCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.2"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2024-06-18T09:07:25.634797491"
+        "timestamp": "2025-12-22T08:44:24.744689029"
     },
     "sarscov2 - fastq": {
         "content": [
@@ -106,14 +114,20 @@
                     "combined_all.txt:md5,9c4de0f90192f410df70076b48659d51"
                 ]
             ],
-            [
-                "versions.yml:md5,e8fcb7ac4528e05b40b58825c13220f0"
-            ]
+            {
+                "versions_ngscheckmate": [
+                    [
+                        "NGSCHECKMATE_VAFNCM",
+                        "ngscheckmate",
+                        "1.0.1"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.4"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-03-05T14:52:07.698272255"
+        "timestamp": "2025-12-21T14:30:44.875730711"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_ngscheckmate/main.nf b/subworkflows/nf-core/bam_ngscheckmate/main.nf
index 33bec39076b2..c68c1c9e9a99 100644
--- a/subworkflows/nf-core/bam_ngscheckmate/main.nf
+++ b/subworkflows/nf-core/bam_ngscheckmate/main.nf
@@ -9,15 +9,12 @@ workflow BAM_NGSCHECKMATE {
     ch_fasta            // channel: [ val(meta3), fasta ]
 
     main:
-
-    ch_versions = channel.empty()
     ch_input_bed = ch_input.combine(ch_snp_bed)
                         .map{ input_meta, input_file, _bed_meta, bed_file ->
                             [input_meta, input_file, bed_file]
                         }
 
     BCFTOOLS_MPILEUP (ch_input_bed, ch_fasta.collect(), false)
-    // Note: bcftools/mpileup versions collected via topic
 
     BCFTOOLS_MPILEUP
     .out
@@ -33,7 +30,6 @@ workflow BAM_NGSCHECKMATE {
     .set {ch_vcfs}
 
     NGSCHECKMATE_NCM (ch_vcfs, ch_snp_bed, ch_fasta)
-    ch_versions = ch_versions.mix(NGSCHECKMATE_NCM.out.versions)
 
     emit:
     corr_matrix  = NGSCHECKMATE_NCM.out.corr_matrix  // channel: [ meta, corr_matrix ]
@@ -41,6 +37,5 @@ workflow BAM_NGSCHECKMATE {
     all          = NGSCHECKMATE_NCM.out.all          // channel: [ meta, all ]
     vcf          = BCFTOOLS_MPILEUP.out.vcf          // channel: [ meta, vcf ]
     pdf          = NGSCHECKMATE_NCM.out.pdf          // channel: [ meta, pdf ]
-    versions     = ch_versions                       // channel: [ versions.yml ]
 
 }
diff --git a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
index baf80178ee79..9452ec104013 100644
--- a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
+++ b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test
@@ -49,8 +49,7 @@ nextflow_workflow {
                     file(workflow.out.matched[0][1]).name,
                     workflow.out.all,
                     workflow.out.vcf.collect {meta, vcf -> path(vcf).vcf.variantsMD5 },
-                    file(workflow.out.pdf[0][1]).name,
-                    workflow.out.versions
+                    file(workflow.out.pdf[0][1]).name
                     ).match()}
             )
         }
@@ -90,8 +89,7 @@ nextflow_workflow {
                     workflow.out.matched,
                     workflow.out.all,
                     workflow.out.vcf.collect {meta, vcf -> path(vcf).vcf.variantsMD5 },
-                    file(workflow.out.pdf[0][1]).name,
-                    workflow.out.versions
+                    file(workflow.out.pdf[0][1]).name
                     ).match()}
             )
         }
diff --git a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
index 59214d4183e7..c9aa26ac676d 100644
--- a/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_ngscheckmate/tests/main.nf.test.snap
@@ -48,9 +48,6 @@
                         "test_bed.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "5": [
-                    "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab"
-                ],
                 "all": [
                     [
                         {
@@ -96,9 +93,6 @@
                         },
                         "test2.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab"
                 ]
             }
         ],
@@ -106,7 +100,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-21T13:57:43.435267089"
+        "timestamp": "2025-12-21T15:52:04.207435157"
     },
     "sarscov2 - cram": {
         "content": [
@@ -138,16 +132,13 @@
                 "d5b1e887b104cd33f18747abd377f47a",
                 "30feeb598a3730af169e3d14c56a05c2"
             ],
-            "test_bed.pdf",
-            [
-                "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab"
-            ]
+            "test_bed.pdf"
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-21T13:57:33.661491799"
+        "timestamp": "2025-12-21T15:51:53.331214361"
     },
     "sarscov2 - bam": {
         "content": [
@@ -172,15 +163,12 @@
                 "9341ed6b9cca02d6b0b822308f4a48c6",
                 "3d6ba59b24dc0a699d9bd5a78bc76869"
             ],
-            "test_bed.pdf",
-            [
-                "versions.yml:md5,73d5516e0d2dd84537b11e5eabcbe3ab"
-            ]
+            "test_bed.pdf"
         ],
         "meta": {
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-21T13:57:23.431285563"
+        "timestamp": "2025-12-21T15:51:41.763998754"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_ngscheckmate/main.nf b/subworkflows/nf-core/fastq_ngscheckmate/main.nf
index bbc6c2d8c059..cb1dc4a4bb0f 100644
--- a/subworkflows/nf-core/fastq_ngscheckmate/main.nf
+++ b/subworkflows/nf-core/fastq_ngscheckmate/main.nf
@@ -7,20 +7,16 @@ workflow FASTQ_NGSCHECKMATE {
     ch_snp_pt // channel: [ val(meta2), snp_pt ]
 
     main:
-    ch_versions = Channel.empty()
-
     NGSCHECKMATE_FASTQ(ch_fastq, ch_snp_pt.first())
-    ch_versions = ch_versions.mix(NGSCHECKMATE_FASTQ.out.versions.first())
 
-    NGSCHECKMATE_FASTQ.out.vaf.map { meta, vaf -> vaf }.collect().map { files -> [files] }.set { ch_collected_vafs }
+    NGSCHECKMATE_FASTQ.out.vaf.map { _meta, vaf -> vaf }.collect().map { files -> [files] }.set { ch_collected_vafs }
 
     ch_snp_pt
-        .map { meta, snp_pt -> meta }
+        .map { meta, _snp_pt -> meta }
         .combine(ch_collected_vafs)
         .set { ch_vafs }
 
     NGSCHECKMATE_VAFNCM(ch_vafs)
-    ch_versions = ch_versions.mix(NGSCHECKMATE_VAFNCM.out.versions.first())
 
     emit:
     corr_matrix = NGSCHECKMATE_VAFNCM.out.corr_matrix // channel: [ meta, corr_matrix ]
@@ -28,5 +24,4 @@ workflow FASTQ_NGSCHECKMATE {
     all         = NGSCHECKMATE_VAFNCM.out.all         // channel: [ meta, all ]
     vaf         = NGSCHECKMATE_FASTQ.out.vaf          // channel: [ meta, vaf ]
     pdf         = NGSCHECKMATE_VAFNCM.out.pdf         // channel: [ meta, pdf ], optional
-    versions    = ch_versions // channel: [ versions.yml ]
 }
diff --git a/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test b/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test
index cd7d033466be..4a61c6881971 100644
--- a/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test
+++ b/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test
@@ -57,8 +57,7 @@ nextflow_workflow {
                     workflow.out.matched,
                     workflow.out.all,
                     workflow.out.vaf,
-                    file(workflow.out.pdf[0][1]).name,
-                    workflow.out.versions
+                    file(workflow.out.pdf[0][1]).name
                     ).match() }
             )
         }
@@ -106,8 +105,7 @@ nextflow_workflow {
             assertAll(
                 { assert workflow.success },
                 { assert snapshot(
-                    workflow.out,
-                    workflow.out.versions.collect{ path(it).yaml }
+                    workflow.out
                 ).match() }
             )
         }
diff --git a/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test.snap
index 4929d4ce4b06..caa27247d5a1 100644
--- a/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_ngscheckmate/tests/main.nf.test.snap
@@ -45,17 +45,13 @@
                     "test3.vaf:md5,ac2723aba980112e818ca0772f80a979"
                 ]
             ],
-            "snp_pt.pdf",
-            [
-                "versions.yml:md5,038afa98e01dd7e7745c5d6fc0adf26e",
-                "versions.yml:md5,6d40d47ec5d9ef29e7e769b6028d9a7b"
-            ]
+            "snp_pt.pdf"
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-05-22T16:11:27.595744588"
+        "timestamp": "2025-12-21T14:42:39.361000999"
     },
     "fastq_ngscheckmate - stub": {
         "content": [
@@ -112,10 +108,6 @@
                         "sarscov2.pdf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "5": [
-                    "versions.yml:md5,038afa98e01dd7e7745c5d6fc0adf26e",
-                    "versions.yml:md5,6d40d47ec5d9ef29e7e769b6028d9a7b"
-                ],
                 "all": [
                     [
                         {
@@ -167,29 +159,13 @@
                         },
                         "test3.vaf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,038afa98e01dd7e7745c5d6fc0adf26e",
-                    "versions.yml:md5,6d40d47ec5d9ef29e7e769b6028d9a7b"
                 ]
-            },
-            [
-                {
-                    "FASTQ_NGSCHECKMATE:NGSCHECKMATE_FASTQ": {
-                        "ngscheckmate": "1.0.1"
-                    }
-                },
-                {
-                    "FASTQ_NGSCHECKMATE:NGSCHECKMATE_VAFNCM": {
-                        "ngscheckmate": "1.0.1"
-                    }
-                }
-            ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-05-22T16:11:41.052843005"
+        "timestamp": "2025-12-21T14:42:49.457638854"
     }
 }
\ No newline at end of file