diff --git a/modules/nf-core/samtools/stats/main.nf b/modules/nf-core/samtools/stats/main.nf
index c06ad3bf67da..f9c1d6378a7f 100644
--- a/modules/nf-core/samtools/stats/main.nf
+++ b/modules/nf-core/samtools/stats/main.nf
@@ -13,8 +13,8 @@ process SAMTOOLS_STATS {
 
     output:
     tuple val(meta), path("*.stats"), emit: stats
-    path  "versions.yml"            , emit: versions
-
+    tuple val("${task.process}"), val('samtools'), eval('samtools version | sed "1!d;s/.* //"'), emit: versions_samtools, topic: versions
+    
     when:
     task.ext.when == null || task.ext.when
 
@@ -28,21 +28,11 @@ process SAMTOOLS_STATS {
         ${reference} \\
         ${input} \\
         > ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}.stats
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/samtools/stats/meta.yml b/modules/nf-core/samtools/stats/meta.yml
index 6dc51885d682..c9358eae3ea4 100644
--- a/modules/nf-core/samtools/stats/meta.yml
+++ b/modules/nf-core/samtools/stats/meta.yml
@@ -55,13 +55,27 @@ output:
           description: File containing samtools stats output
           pattern: "*.{stats}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_samtools:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - samtools:
+          type: string
+          description: Name of the tool
+      - samtools version | sed "1!d;s/.* //:
+          type: string
+          description: The command used to generate the version of the tool
+topics:
+  - versions:
+      - - process:
+            type: string
+            description: The process the versions were collected from
+        - tool:
+            type: string
+            description: The tool name
+        - version:
+            type: string
+            description: The version of the tool
 authors:
   - "@drpatelh"
   - "@FriederikeHanssen"
diff --git a/modules/nf-core/samtools/stats/tests/main.nf.test.snap b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
index a451c04e68fd..94d981b2ab21 100644
--- a/modules/nf-core/samtools/stats/tests/main.nf.test.snap
+++ b/modules/nf-core/samtools/stats/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "stats": [
                     [
@@ -23,16 +27,20 @@
                         "test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T15:05:52.878044"
+        "timestamp": "2025-11-01T02:27:18.460724"
     },
     "bam - stub": {
         "content": [
@@ -47,7 +55,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "stats": [
                     [
@@ -58,16 +70,20 @@
                         "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T15:05:56.722672"
+        "timestamp": "2025-11-01T02:27:30.245839"
     },
     "cram - stub": {
         "content": [
@@ -82,7 +98,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "stats": [
                     [
@@ -93,16 +113,20 @@
                         "test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T15:06:13.766719"
+        "timestamp": "2025-11-01T02:27:39.041649"
     },
     "bam": {
         "content": [
@@ -117,7 +141,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ],
                 "stats": [
                     [
@@ -128,15 +156,19 @@
                         "test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
+                "versions_samtools": [
+                    [
+                        "SAMTOOLS_STATS",
+                        "samtools",
+                        "1.22.1"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T15:05:30.301153"
+        "timestamp": "2025-11-01T02:26:55.988241"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
index d4c6c0b58caa..a4aad63142ae 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
@@ -22,15 +22,14 @@
                 "versions.yml:md5,15a99b83c8965f9b29d0e9e6dbdef621",
                 "versions.yml:md5,61bd927f2f2121e34d94692a62305955",
                 "versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
-                "versions.yml:md5,67313fdb9b1b2ccee1c00408cc7ae072",
                 "versions.yml:md5,71d8ff70a0f65311659c446278f10b1a"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:32:36.702719"
+        "timestamp": "2025-11-01T02:35:06.350407"
     },
     "test_bam_dedup_stats_samtools_umicollapse_flagstats": {
         "content": [
diff --git a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
index fcacab888c9f..91045746bbee 100644
--- a/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
@@ -28,17 +28,16 @@
             ],
             [
                 "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
-                "versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
                 "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
                 "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
                 "versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T09:42:03.400348"
+        "timestamp": "2025-11-01T02:35:42.524116"
     },
     "sarscov2_bam_bai - stub": {
         "content": [
@@ -83,7 +82,7 @@
                         {
                             "id": "test"
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "6": [
@@ -96,7 +95,6 @@
                 ],
                 "7": [
                     "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
-                    "versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
                     "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
                     "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
                     "versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
@@ -133,7 +131,7 @@
                         {
                             "id": "test"
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -154,7 +152,6 @@
                 ],
                 "versions": [
                     "versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
-                    "versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
                     "versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
                     "versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
                     "versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
@@ -162,9 +159,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T09:42:13.338671"
+        "timestamp": "2025-11-01T02:35:58.59434"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
index 67a0fe7e33ff..5e24e12bc7cb 100644
--- a/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_markduplicates_picard/tests/main.nf.test.snap
@@ -9,16 +9,15 @@
             [
                 "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                 "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                 "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                 "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:56:16.015907189"
+        "timestamp": "2025-11-01T02:37:26.3247"
     },
     "sarscov2 - bam - stub": {
         "content": [
@@ -74,7 +73,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "8": [
@@ -89,7 +88,6 @@
                 "9": [
                     "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                     "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                    "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                     "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                     "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
                 ],
@@ -126,7 +124,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -159,17 +157,16 @@
                 "versions": [
                     "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                     "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                    "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                     "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                     "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:56:28.143938191"
+        "timestamp": "2025-11-01T02:37:50.805524"
     },
     "homo_sapiens - cram - stub": {
         "content": [
@@ -220,7 +217,7 @@
                         {
                             "id": "test"
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "8": [
@@ -234,7 +231,6 @@
                 "9": [
                     "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                     "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                    "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                     "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                     "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
                 ],
@@ -268,7 +264,7 @@
                         {
                             "id": "test"
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -298,17 +294,16 @@
                 "versions": [
                     "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                     "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                    "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                     "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                     "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:56:40.395713551"
+        "timestamp": "2025-11-01T02:38:18.069303"
     },
     "sarscov2 - bam": {
         "content": [
@@ -320,15 +315,14 @@
             [
                 "versions.yml:md5,492bf2c795ed7c31947f0390a5b6cbe1",
                 "versions.yml:md5,53f9c88ce12ea1192cf2fb12cb3f980f",
-                "versions.yml:md5,cccd7bb84a8caecd7558214c09f0a264",
                 "versions.yml:md5,d298dab7f84d3fa45618d3be5c054a92",
                 "versions.yml:md5,fb2919b16758582cf470a86acd1f1886"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T10:56:01.213524305"
+        "timestamp": "2025-11-01T02:36:56.78063"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_markduplicates_samtools/main.nf b/subworkflows/nf-core/bam_markduplicates_samtools/main.nf
index 2d097179c4e5..5bb663694fed 100644
--- a/subworkflows/nf-core/bam_markduplicates_samtools/main.nf
+++ b/subworkflows/nf-core/bam_markduplicates_samtools/main.nf
@@ -26,7 +26,6 @@ workflow BAM_MARKDUPLICATES_SAMTOOLS {
     ch_versions = ch_versions.mix(SAMTOOLS_FIXMATE.out.versions)
 
     SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam, ch_fasta, '' )
-    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions)
 
     SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, ch_fasta )
     ch_versions = ch_versions.mix(SAMTOOLS_MARKDUP.out.versions)
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
index 4607263684d7..ccef09d88bdf 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/main.nf
@@ -16,7 +16,6 @@ workflow BAM_SORT_STATS_SAMTOOLS {
     ch_versions = Channel.empty()
 
     SAMTOOLS_SORT ( ch_bam, ch_fasta, '' )
-    ch_versions = ch_versions.mix(SAMTOOLS_SORT.out.versions.first())
 
     SAMTOOLS_INDEX ( SAMTOOLS_SORT.out.bam )
     ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
diff --git a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap
index 1cc7fa3d6c7f..239f163c79d3 100644
--- a/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_sort_stats_samtools/tests/main.nf.test.snap
@@ -29,18 +29,16 @@
                 ]
             ],
             [
-                "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                 "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                 "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                 "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:37:01.228228"
+        "timestamp": "2025-11-01T03:04:39.140333"
     },
     "test_bam_sort_stats_samtools_paired_end": {
         "content": [
@@ -72,18 +70,16 @@
                 ]
             ],
             [
-                "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                 "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                 "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                 "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:37:08.591748"
+        "timestamp": "2025-11-01T03:04:48.787289"
     },
     "test_bam_sort_stats_samtools_single_end - stub": {
         "content": [
@@ -124,7 +120,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "5": [
@@ -137,10 +133,8 @@
                     ]
                 ],
                 "6": [
-                    "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                     "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                     "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                    "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                     "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
                 ],
                 "bai": [
@@ -170,7 +164,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -192,19 +186,17 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                     "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                     "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                    "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                     "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:37:15.315753"
+        "timestamp": "2025-11-01T03:05:00.693649"
     },
     "test_bam_sort_stats_samtools_paired_end - stub": {
         "content": [
@@ -245,7 +237,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "5": [
@@ -258,10 +250,8 @@
                     ]
                 ],
                 "6": [
-                    "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                     "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                     "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                    "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                     "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
                 ],
                 "bai": [
@@ -291,7 +281,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -313,18 +303,16 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,199b33608db0a9457645d070ab24b71b",
                     "versions.yml:md5,54f02345c3a7699f9272e6ef9ce916c5",
                     "versions.yml:md5,6a93080732801bacb21c3acbe13858a5",
-                    "versions.yml:md5,8f2a377b0149cf437f0730d293b62c81",
                     "versions.yml:md5,de3b0ae7c3ac4188662d57fd3219e312"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:37:22.163708"
+        "timestamp": "2025-11-01T03:05:10.863912"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/bam_stats_samtools/main.nf b/subworkflows/nf-core/bam_stats_samtools/main.nf
index 44d4c010a2fe..90fcbf80c47d 100644
--- a/subworkflows/nf-core/bam_stats_samtools/main.nf
+++ b/subworkflows/nf-core/bam_stats_samtools/main.nf
@@ -15,7 +15,6 @@ workflow BAM_STATS_SAMTOOLS {
     ch_versions = Channel.empty()
 
     SAMTOOLS_STATS ( ch_bam_bai, ch_fasta )
-    ch_versions = ch_versions.mix(SAMTOOLS_STATS.out.versions)
 
     SAMTOOLS_FLAGSTAT ( ch_bam_bai )
     ch_versions = ch_versions.mix(SAMTOOLS_FLAGSTAT.out.versions)
diff --git a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
index dadc71a7100f..3c543191d92b 100644
--- a/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/bam_stats_samtools/tests/main.nf.test.snap
@@ -31,8 +31,7 @@
                 ],
                 "3": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ],
                 "flagstat": [
                     [
@@ -63,16 +62,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:35.417926"
+        "timestamp": "2025-11-01T02:39:28.707989"
     },
     "test_bam_stats_samtools_single_end - stub": {
         "content": [
@@ -106,8 +104,7 @@
                 ],
                 "3": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ],
                 "flagstat": [
                     [
@@ -138,16 +135,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:25.439222"
+        "timestamp": "2025-11-01T02:39:20.473816"
     },
     "test_bam_stats_samtools_paired_end_cram - stub": {
         "content": [
@@ -181,8 +177,7 @@
                 ],
                 "3": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ],
                 "flagstat": [
                     [
@@ -213,16 +208,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                    "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                    "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:46.02738"
+        "timestamp": "2025-11-01T02:39:37.697552"
     },
     "test_bam_stats_samtools_single_end": {
         "content": [
@@ -255,15 +249,14 @@
             ],
             [
                 "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:00.064679"
+        "timestamp": "2025-11-01T02:38:50.143087"
     },
     "test_bam_stats_samtools_paired_end": {
         "content": [
@@ -296,15 +289,14 @@
             ],
             [
                 "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:08.141202"
+        "timestamp": "2025-11-01T02:39:01.02311"
     },
     "test_bam_stats_samtools_paired_end_cram": {
         "content": [
@@ -337,14 +329,13 @@
             ],
             [
                 "versions.yml:md5,088c14fc7d21fa2e662860d7cbf9a181",
-                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa",
-                "versions.yml:md5,c7826ee705b3af5245db8d9cf64ed520"
+                "versions.yml:md5,ade6457ea5ae73a41c505bb22681d0fa"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-15T15:20:16.06318"
+        "timestamp": "2025-11-01T02:39:12.503355"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
index 8cb4cacdc5aa..1e9c916bcdcc 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/main.nf
@@ -64,7 +64,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH {
         ''
     )
     ch_alignment = SAMTOOLS_SORT.out.bam
-    ch_versions  = ch_versions.mix(SAMTOOLS_SORT.out.versions)
 
     /*
      * Run samtools index on alignment
@@ -92,7 +91,6 @@ workflow FASTQ_ALIGN_DEDUP_BWAMETH {
         [[:],[]] // [ [meta], [fasta]]
     )
     ch_samtools_stats = SAMTOOLS_STATS.out.stats
-    ch_versions       = ch_versions.mix(SAMTOOLS_STATS.out.versions)
 
     if (!skip_deduplication) {
         /*
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap
index d4b27da21fe8..021c089e3262 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/gpu.nf.test.snap
@@ -34,11 +34,9 @@
                 "test.stats"
             ],
             [
-                "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43",
                 "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e",
                 "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85",
                 "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f",
-                "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb",
                 "versions.yml:md5,e9c5078a84e09a78756e7f9a5b1a9f89",
                 "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c"
             ]
@@ -47,7 +45,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.8"
         },
-        "timestamp": "2025-10-13T16:57:26.654134509"
+        "timestamp": "2025-11-03T10:01:41.475172082"
     },
     "Params: parabricks/fq2bammeth single-end | use_gpu | skip_deduplication": {
         "content": [
@@ -83,10 +81,8 @@
                 "test.stats"
             ],
             [
-                "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43",
                 "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e",
                 "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f",
-                "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb",
                 "versions.yml:md5,e9c5078a84e09a78756e7f9a5b1a9f89"
             ]
         ],
@@ -94,6 +90,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.04.8"
         },
-        "timestamp": "2025-10-13T16:58:18.600891908"
+        "timestamp": "2025-11-03T10:02:53.402903725"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
index 6ad8ba50c89a..61d72a8439fa 100644
--- a/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_align_dedup_bwameth/tests/main.nf.test.snap
@@ -34,20 +34,18 @@
                 "test.stats"
             ],
             [
-                "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43",
                 "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e",
                 "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85",
                 "versions.yml:md5,6c757564e855659911e8721c78ef6303",
                 "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f",
-                "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb",
                 "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-16T19:27:14.082839334"
+        "timestamp": "2025-11-01T03:09:53.217361"
     },
     "Params: bwameth paired-end | skip_deduplication": {
         "content": [
@@ -83,18 +81,16 @@
                 "test.stats"
             ],
             [
-                "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43",
                 "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e",
                 "versions.yml:md5,6c757564e855659911e8721c78ef6303",
-                "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f",
-                "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb"
+                "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-16T19:27:38.015666411"
+        "timestamp": "2025-11-01T03:10:41.87614"
     },
     "Params: bwameth paired-end | default": {
         "content": [
@@ -131,19 +127,17 @@
                 "test.stats"
             ],
             [
-                "versions.yml:md5,41792ca650dbdef82bb7f7d2ad60ae43",
                 "versions.yml:md5,48be1c2cdf91f79fe53d2d5397990e6e",
                 "versions.yml:md5,58f62eabbc05b725b68ae05ad2adab85",
                 "versions.yml:md5,6c757564e855659911e8721c78ef6303",
                 "versions.yml:md5,774d8bec22bddd6b837e4e2c458dcb7f",
-                "versions.yml:md5,ad58eef75d509ee0c8325ce60659a4fb",
                 "versions.yml:md5,f3b8471451c0aab08b19ca4f19d09b7c"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-16T19:27:27.812652475"
+        "timestamp": "2025-11-01T03:10:25.929797"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap
index 0c5ff18a6989..149d7dfbaa08 100644
--- a/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/fastq_align_hisat2/tests/main.nf.test.snap
@@ -47,19 +47,17 @@
                 ]
             ],
             [
-                "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                 "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                 "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                 "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                 "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:45:52.568487"
+        "timestamp": "2025-11-01T03:11:11.528432"
     },
     "sarscov2 - bam - single_end - stub": {
         "content": [
@@ -121,7 +119,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "8": [
@@ -134,9 +132,7 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                     "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                    "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                     "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                     "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                     "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
@@ -171,7 +167,7 @@
                             "id": "test",
                             "single_end": true
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -211,9 +207,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                     "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                    "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                     "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                     "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                     "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
@@ -221,10 +215,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:46:19.202781"
+        "timestamp": "2025-11-01T03:11:57.586261"
     },
     "sarscov2 - bam - paired_end": {
         "content": [
@@ -274,19 +268,17 @@
                 ]
             ],
             [
-                "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                 "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                 "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                 "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                 "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:46:05.340425"
+        "timestamp": "2025-11-01T03:11:28.95845"
     },
     "sarscov2 - bam - paired_end - stub": {
         "content": [
@@ -348,7 +340,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "8": [
@@ -361,9 +353,7 @@
                     ]
                 ],
                 "9": [
-                    "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                     "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                    "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                     "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                     "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                     "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
@@ -398,7 +388,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
                     ]
                 ],
                 "idxstats": [
@@ -438,9 +428,7 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,06ff7cd2d71052a116593358ae354acf",
                     "versions.yml:md5,18dfb578b63a4c06df9029d214d26b21",
-                    "versions.yml:md5,467226d098f9c06ff09a65d7d5f5a489",
                     "versions.yml:md5,6a468ef612faa1b6419ef5688c0c760f",
                     "versions.yml:md5,e0481c30dd24b96ee2ace998a360ea29",
                     "versions.yml:md5,ec6468a88403ffc733629109b26e2484"
@@ -448,9 +436,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-10T13:46:31.990062"
+        "timestamp": "2025-11-01T03:12:21.057787"
     }
 }
\ No newline at end of file