diff --git a/modules/nf-core/pmdtools/filter/environment.yml b/modules/nf-core/pmdtools/filter/environment.yml
index 056c22dd7e61..77053ebdf6cd 100644
--- a/modules/nf-core/pmdtools/filter/environment.yml
+++ b/modules/nf-core/pmdtools/filter/environment.yml
@@ -6,3 +6,4 @@ channels:
 dependencies:
   - bioconda::pmdtools=0.60
   - bioconda::samtools=1.14
+  - conda-forge::python=3.9.7
diff --git a/modules/nf-core/pmdtools/filter/main.nf b/modules/nf-core/pmdtools/filter/main.nf
index 97f2b5b72e05..aecd390a263b 100644
--- a/modules/nf-core/pmdtools/filter/main.nf
+++ b/modules/nf-core/pmdtools/filter/main.nf
@@ -14,7 +14,8 @@ process PMDTOOLS_FILTER {
 
     output:
     tuple val(meta), path("*.bam"), emit: bam
-    path "versions.yml"               , emit: versions
+    tuple val("${task.process}"), val('pmdtools'), eval("pmdtools --version | sed 's/.*v//'")  , topic: versions, emit: versions_pmdtools
+    tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools
 
     when:
     task.ext.when == null || task.ext.when
@@ -25,45 +26,33 @@ process PMDTOOLS_FILTER {
     def args3 = task.ext.args3 ?: ''
     def split_cpus = Math.floor(task.cpus/2)
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${bam}" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     //threshold and header flags activate filtering function of pmdtools
     """
     samtools \\
         calmd \\
-        $bam \\
-        $reference \\
-        $args \\
+        ${bam} \\
+        ${reference} \\
+        ${args} \\
         -@ ${split_cpus} \\
     | pmdtools \\
-        --threshold $threshold \\
+        --threshold ${threshold} \\
         --header \\
-        $args2 \\
+        ${args2} \\
     | samtools \\
         view \\
-        $args3 \\
+        ${args3} \\
         -Sb \\
         - \\
         -@ ${split_cpus} \\
         -o ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pmdtools: \$( pmdtools --version | cut -f2 -d ' ' | sed 's/v//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
-    if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
+    if ("${bam}" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
     //threshold and header flags activate filtering function of pmdtools
     """
     touch ${prefix}.bam
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        pmdtools: \$( pmdtools --version | cut -f2 -d ' ' | sed 's/v//')
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/pmdtools/filter/meta.yml b/modules/nf-core/pmdtools/filter/meta.yml
index 05da0dc434cf..e780d4a35409 100644
--- a/modules/nf-core/pmdtools/filter/meta.yml
+++ b/modules/nf-core/pmdtools/filter/meta.yml
@@ -12,7 +12,8 @@ tools:
       documentation: https://github.com/pontussk/PMDtools
       tool_dev_url: https://github.com/pontussk/PMDtools
       doi: "10.1073/pnas.1318934111"
-      licence: ["GPL v3"]
+      licence:
+        - "GPL v3"
       identifier: ""
 input:
   - - meta:
@@ -50,13 +51,50 @@ output:
           description: Filtered BAM file
           pattern: "*.bam"
           ontologies: []
+  versions_pmdtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - pmdtools:
+          type: string
+          description: The name of the tool
+      - pmdtools --version | sed 's/.*v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          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
+      - pmdtools:
+          type: string
+          description: The name of the tool
+      - pmdtools --version | sed 's/.*v//':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - samtools:
+          type: string
+          description: The name of the tool
+      - samtools version | sed '1!d;s/.* //':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@alexandregilardet"
 maintainers:
diff --git a/modules/nf-core/pmdtools/filter/tests/main.nf.test b/modules/nf-core/pmdtools/filter/tests/main.nf.test
index d8fa6a13cf99..2631b539c20b 100644
--- a/modules/nf-core/pmdtools/filter/tests/main.nf.test
+++ b/modules/nf-core/pmdtools/filter/tests/main.nf.test
@@ -16,13 +16,12 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
-				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-				input[1] = 3
-				input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
-
+                input[1] = 3
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 """
             }
         }
@@ -31,11 +30,9 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(
-					bam(process.out.bam[0][1]).getReadsMD5(),
-					process.out.versions,
-                    file(process.out.versions[0]).readLines()[1..2].collect { it.trim() } // Trap to catch conda version mismatches
-					).match()
-				}
+                    bam(process.out.bam[0][1]).getReadsMD5(),
+                    sanitizeOutput(process.out, unstableKeys:["bam"])
+                ).match()}
             )
         }
     }
@@ -47,13 +44,12 @@ nextflow_process {
             process {
                 """
                 input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
-				    [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
                 ]
-				input[1] = 3
-				input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]
-
+                input[1] = 3
+                input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
                 """
             }
         }
@@ -61,7 +57,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }
diff --git a/modules/nf-core/pmdtools/filter/tests/main.nf.test.snap b/modules/nf-core/pmdtools/filter/tests/main.nf.test.snap
index 9746297980a3..c53fd0d06f82 100644
--- a/modules/nf-core/pmdtools/filter/tests/main.nf.test.snap
+++ b/modules/nf-core/pmdtools/filter/tests/main.nf.test.snap
@@ -2,53 +2,68 @@
     "test-pmdtools-filter": {
         "content": [
             "665610db11378e0a02ab7d407a9d54c1",
-            [
-                "versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
-            ],
-            [
-                "pmdtools: 0.50",
-                "samtools: 1.14"
-            ]
+            {
+                "bam": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.bam"
+                    ]
+                ],
+                "versions_pmdtools": [
+                    [
+                        "PMDTOOLS_FILTER",
+                        "pmdtools",
+                        "0.50"
+                    ]
+                ],
+                "versions_samtools": [
+                    [
+                        "PMDTOOLS_FILTER",
+                        "samtools",
+                        "1.14"
+                    ]
+                ]
+            }
         ],
+        "timestamp": "2026-08-06T15:52:16.062661885",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T12:54:08.428303"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     },
     "test-pmdtools-filter-stub": {
         "content": [
             {
-                "0": [
+                "bam": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
                         "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "1": [
-                    "versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
-                ],
-                "bam": [
+                "versions_pmdtools": [
                     [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "PMDTOOLS_FILTER",
+                        "pmdtools",
+                        "0.50"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
+                "versions_samtools": [
+                    [
+                        "PMDTOOLS_FILTER",
+                        "samtools",
+                        "1.14"
+                    ]
                 ]
             }
         ],
+        "timestamp": "2026-08-06T15:52:22.821082671",
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "24.04.4"
-        },
-        "timestamp": "2024-08-29T12:40:43.138953"
+            "nf-test": "0.9.5",
+            "nextflow": "26.04.6"
+        }
     }
 }
\ No newline at end of file