diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 325b8bbff8af..220a0b6cca73 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -11,9 +11,9 @@ process TABIX_TABIX {
     tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("*.tbi"), optional:true, emit: tbi
-    tuple val(meta), path("*.csi"), optional:true, emit: csi
-    path  "versions.yml"          , emit: versions
+    tuple val(meta), path("*.tbi")                                                                          , optional:true     , emit: tbi
+    tuple val(meta), path("*.csi")                                                                          , optional:true     , emit: csi
+    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
 
     when:
     task.ext.when == null || task.ext.when
@@ -26,20 +26,10 @@ process TABIX_TABIX {
         $args \\
         $tab
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
-
     stub:
     """
     touch ${tab}.tbi
     touch ${tab}.csi
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index c172968d87f9..8e84813cb220 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -46,13 +46,27 @@ output:
           description: coordinate sorted index file
           pattern: "*.{csi}"
           ontologies: []
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software versions
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_tabix:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - tabix:
+          type: string
+          description: The tool name
+      - tabix -h 2>&1 | tail -1:
+          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:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index e74afd926d47..8ba227bf2760 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -27,7 +27,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out,
-                    file(process.out.tbi[0][1]).name
+                    file(process.out.tbi[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
@@ -51,7 +52,9 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out,
-                    file(process.out.tbi[0][1]).name).match() }
+                    file(process.out.tbi[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
             )
         }
 
@@ -75,7 +78,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out,
-                    file(process.out.tbi[0][1]).name
+                    file(process.out.tbi[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
@@ -100,7 +104,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out,
-                    file(process.out.csi[0][1]).name
+                    file(process.out.csi[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
@@ -126,11 +131,11 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out,
-                    file(process.out.csi[0][1]).name
+                    file(process.out.csi[0][1]).name,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
                 ).match() }
             )
         }
-
     }
 
 }
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
index 67b8e3c2f9ec..d05a2f8585d5 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -14,7 +14,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "csi": [
                     
@@ -27,17 +31,30 @@
                         "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             },
-            "genome.gff3.gz.tbi"
+            "genome.gff3.gz.tbi",
+            {
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-26T13:52:48.638506004"
+        "timestamp": "2025-10-29T15:30:55.967501479"
     },
     "sarscov2_bedgz_tbi": {
         "content": [
@@ -54,7 +71,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "csi": [
                     
@@ -67,17 +88,30 @@
                         "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             },
-            "test.bed.gz.tbi"
+            "test.bed.gz.tbi",
+            {
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-26T13:52:44.910707349"
+        "timestamp": "2025-10-29T15:30:50.90188633"
     },
     "sarscov2_vcf_tbi": {
         "content": [
@@ -94,7 +128,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "csi": [
                     
@@ -107,17 +145,30 @@
                         "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             },
-            "test.vcf.gz.tbi"
+            "test.vcf.gz.tbi",
+            {
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-26T13:52:52.405662623"
+        "timestamp": "2025-10-29T15:31:00.935418897"
     },
     "sarscov2_vcf_csi_stub": {
         "content": [
@@ -139,7 +190,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "csi": [
                     [
@@ -157,17 +212,30 @@
                         "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             },
-            "test.vcf.gz.csi"
+            "test.vcf.gz.csi",
+            {
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-26T13:52:59.633992323"
+        "timestamp": "2025-10-29T15:31:10.669125187"
     },
     "sarscov2_vcf_csi": {
         "content": [
@@ -184,7 +252,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "csi": [
                     [
@@ -197,16 +269,29 @@
                 "tbi": [
                     
                 ],
-                "versions": [
-                    "versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             },
-            "test.vcf.gz.csi"
+            "test.vcf.gz.csi",
+            {
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-03-26T13:52:56.083553332"
+        "timestamp": "2025-10-29T15:31:05.605794542"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
index 4d3e89e243f6..039ed84bf312 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
@@ -34,7 +34,6 @@ workflow VCF_ANNOTATE_ENSEMBLVEP {
 
     // Gather versions of all tools used
     ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions)
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
 
     emit:
     vcf_tbi  = ch_vcf_tbi // channel: [ val(meta), path(vcf), path(tbi) ]
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap
index a9a807e8e3cd..772b058a2ccd 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep/tests/main.nf.test.snap
@@ -14,15 +14,14 @@
                 "test.vep.vcf.gz_summary.html"
             ],
             [
-                "versions.yml:md5,d8b556eea76d3089dcdc6e5c3931cafc",
                 "versions.yml:md5,de6e873a7f1613f407477d0217a767d4"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-29T10:01:03.370604"
+        "timestamp": "2025-10-28T16:17:48.298505646"
     },
     "WBcel235 caenorhabditis_elegans 114 - test.vcf.gz - stub": {
         "content": [
@@ -46,7 +45,6 @@
                     "test.vep_summary.html:md5,d41d8cd98f00b204e9800998ecf8427e"
                 ],
                 "4": [
-                    "versions.yml:md5,d8b556eea76d3089dcdc6e5c3931cafc",
                     "versions.yml:md5,de6e873a7f1613f407477d0217a767d4"
                 ],
                 "json": [
@@ -68,15 +66,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,d8b556eea76d3089dcdc6e5c3931cafc",
                     "versions.yml:md5,de6e873a7f1613f407477d0217a767d4"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.7"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-29T10:01:14.27719"
+        "timestamp": "2025-10-28T16:18:03.840499946"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
index 9829b319f96d..977d4be337c0 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -130,6 +130,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
             SNPEFF_SNPEFF.out.vcf
         )
         ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first())
+        
         ch_snpeff_output = TABIX_BGZIP.out.output
     } else {
         ch_snpeff_output  = ch_vep_output
@@ -187,7 +188,6 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
     TABIX_TABIX(
         ch_tabix_input.bgzip
     )
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
 
     def ch_vcf_tbi = ch_tabix_input.bgzip
         .join(TABIX_TABIX.out.tbi, failOnDuplicate: true, failOnMismatch: true)
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap
index 60022e0bf591..ca7e77dcad50 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/tests/main.nf.test.snap
@@ -123,16 +123,14 @@
                 "versions.yml",
                 "versions.yml",
                 "versions.yml",
-                "versions.yml",
-                "versions.yml",
                 "versions.yml"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-21T14:26:15.070353824"
+        "timestamp": "2025-10-29T11:42:55.57866235"
     },
     "sarscov2 - ensemblvep - large chunks": {
         "content": [
@@ -165,15 +163,14 @@
                 "versions.yml",
                 "versions.yml",
                 "versions.yml",
-                "versions.yml",
                 "versions.yml"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-21T14:30:24.298758636"
+        "timestamp": "2025-10-28T15:05:08.526580844"
     },
     "sarscov2 - snpeff + ensemblvep": {
         "content": [
@@ -248,15 +245,14 @@
                 "versions.yml",
                 "versions.yml",
                 "versions.yml",
-                "versions.yml",
                 "versions.yml"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-21T14:27:10.331672866"
+        "timestamp": "2025-10-29T11:43:20.014782103"
     },
     "sarscov2 - ensemblvep - no scatter": {
         "content": [
@@ -283,15 +279,14 @@
                 
             ],
             [
-                "versions.yml",
                 "versions.yml"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-21T14:30:56.234362683"
+        "timestamp": "2025-10-28T15:05:34.860678122"
     },
     "sarscov2 - ensemblvep": {
         "content": [
@@ -325,14 +320,13 @@
                 "versions.yml",
                 "versions.yml",
                 "versions.yml",
-                "versions.yml",
                 "versions.yml"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-08-21T14:21:26.819889208"
+        "timestamp": "2025-10-28T15:03:18.747847891"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
index 6d41a399e07f..760982168de8 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
@@ -27,8 +27,6 @@ workflow VCF_EXTRACT_RELATE_SOMALIER {
         ch_input.no_tbi
     )
 
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
-
     ch_somalierextract_input = ch_input.no_tbi
         .join(TABIX_TABIX.out.tbi)
         .mix(ch_input.tbi)
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test.snap
index 7fa907dae6fc..f60881f6667b 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/tests/main.nf.test.snap
@@ -109,7 +109,7 @@
                         {
                             "id": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "3": [
@@ -117,7 +117,7 @@
                         {
                             "id": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "4": [
@@ -148,7 +148,7 @@
                         {
                             "id": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "samples_tsv": [
@@ -156,7 +156,7 @@
                         {
                             "id": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "versions": [
@@ -166,10 +166,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:22:29.062966"
+        "timestamp": "2025-10-28T15:00:51.457448603"
     },
     "homo_sapiens minimal - vcf 1 - fasta - fai - sites - [] - [] - []": {
         "content": [
@@ -208,8 +208,7 @@
                 ],
                 "4": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -245,16 +244,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-21T11:36:57.412934244"
+        "timestamp": "2025-10-28T14:59:31.767337684"
     },
     "homo_sapiens mixed_combine_no_count- [vcf, vcf] [index, []] [] - fasta - fai - sites - ped - samples - common": {
         "content": [
@@ -290,7 +288,7 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "3": [
@@ -299,14 +297,13 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "4": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -339,7 +336,7 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "samples_tsv": [
@@ -348,22 +345,21 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:22:36.406311"
+        "timestamp": "2025-10-28T15:01:06.471227992"
     },
     "homo_sapiens mixed_combine - [vcf, vcf] [index, []] 2 - fasta - fai - sites - ped - samples - common": {
         "content": [
@@ -399,7 +395,7 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "3": [
@@ -408,14 +404,13 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "4": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -448,7 +443,7 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.pairs.tsv:md5,5ca81178a364537967c21d55029e7db3"
+                        "test.pairs.tsv:md5,f34e11f0c67615be91afca8379d03ca5"
                     ]
                 ],
                 "samples_tsv": [
@@ -457,22 +452,21 @@
                             "id": "test",
                             "common": "test"
                         },
-                        "test.samples.tsv:md5,d94b949ae26aa748437d55f8ca1fd9eb"
+                        "test.samples.tsv:md5,63938fbed12480ca48a05ee42315298b"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:22:14.373857"
+        "timestamp": "2025-10-28T15:00:16.722060909"
     },
     "homo_sapiens mixed_no_combine - [vcf, vcf] [index, []] 1 - fasta - fai - sites - [ped, ped] - [] - []": {
         "content": [
@@ -524,7 +518,7 @@
                         {
                             "id": "test2"
                         },
-                        "test2.samples.tsv:md5,fec95e92b813e85a480a5e0178ef47c5"
+                        "test2.samples.tsv:md5,ff3aa68dffa5582de08779f513935960"
                     ],
                     [
                         {
@@ -537,8 +531,7 @@
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -587,7 +580,7 @@
                         {
                             "id": "test2"
                         },
-                        "test2.samples.tsv:md5,fec95e92b813e85a480a5e0178ef47c5"
+                        "test2.samples.tsv:md5,ff3aa68dffa5582de08779f513935960"
                     ],
                     [
                         {
@@ -600,16 +593,15 @@
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:22:21.644458"
+        "timestamp": "2025-10-28T15:00:31.98387191"
     },
     "homo_sapiens with_ped - vcf 1 - fasta - fai - sites - ped - [] - []": {
         "content": [
@@ -648,8 +640,7 @@
                 ],
                 "4": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -685,16 +676,15 @@
                 ],
                 "versions": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-21T11:40:37.745314043"
+        "timestamp": "2025-10-28T15:00:01.07237171"
     },
     "homo_sapiens mixed_combine_no_count- [vcf, vcf] [index, []] [] - fasta - fai - sites - ped - samples - common -- stub": {
         "content": [
@@ -745,8 +735,7 @@
                 "4": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ],
                 "extract": [
                     [
@@ -794,8 +783,7 @@
                 "versions": [
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
                     "versions.yml:md5,1affbf55dcb6f7bc394ebc6ba8d32eaa",
-                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940",
-                    "versions.yml:md5,2be58dcf43db0e2b3be1a5f86b96cc45"
+                    "versions.yml:md5,218f8c413e2214d0ec3c37ce942c6940"
                 ]
             },
             [
@@ -813,18 +801,13 @@
                     "VCF_EXTRACT_RELATE_SOMALIER:SOMALIER_RELATE": {
                         "somalier": "0.2.19"
                     }
-                },
-                {
-                    "VCF_EXTRACT_RELATE_SOMALIER:TABIX_TABIX": {
-                        "tabix": 1.21
-                    }
                 }
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-05-21T12:04:35.662979343"
+        "timestamp": "2025-10-28T15:01:20.159960568"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_gather_bcftools/main.nf b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
index a231ebf8638e..3c2f4d94bf5a 100644
--- a/subworkflows/nf-core/vcf_gather_bcftools/main.nf
+++ b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
@@ -35,7 +35,6 @@ workflow VCF_GATHER_BCFTOOLS {
     }
 
     TABIX_TABIX ( ch_tabix_input )
-    ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)
 
     emit:
     vcf      = ch_tabix_input        // channel: [ val(meta), [ vcf ] ]
diff --git a/subworkflows/nf-core/vcf_gather_bcftools/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_gather_bcftools/tests/main.nf.test.snap
index 00c836e5e970..67826c52db41 100644
--- a/subworkflows/nf-core/vcf_gather_bcftools/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_gather_bcftools/tests/main.nf.test.snap
@@ -9,15 +9,14 @@
             ],
             [
                 "versions.yml:md5,6ea8d5a86ac40fb95744d48b345d73ae",
-                "versions.yml:md5,a1f631d2e625bc6eeba98485d6f36f3b",
                 "versions.yml:md5,f6684e4389f67f8f626c17812f368ace"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:08:09.860182"
+        "timestamp": "2025-10-28T15:17:22.250313382"
     },
     "homo_sapiens no_meta - [vcf, tbi] [vcf, tbi] - meta equal [] 2 - [] - true": {
         "content": [
@@ -29,15 +28,14 @@
             ],
             [
                 "versions.yml:md5,6ea8d5a86ac40fb95744d48b345d73ae",
-                "versions.yml:md5,a1f631d2e625bc6eeba98485d6f36f3b",
                 "versions.yml:md5,f6684e4389f67f8f626c17812f368ace"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:08:17.638136"
+        "timestamp": "2025-10-28T15:17:39.808134162"
     },
     "homo_sapiens no_meta - [vcf, tbi] [vcf, tbi] - meta equal [] 2 - [] - true -- stub": {
         "content": [
@@ -60,7 +58,6 @@
                 ],
                 "2": [
                     "versions.yml:md5,6ea8d5a86ac40fb95744d48b345d73ae",
-                    "versions.yml:md5,a1f631d2e625bc6eeba98485d6f36f3b",
                     "versions.yml:md5,f6684e4389f67f8f626c17812f368ace"
                 ],
                 "tbi": [
@@ -81,7 +78,6 @@
                 ],
                 "versions": [
                     "versions.yml:md5,6ea8d5a86ac40fb95744d48b345d73ae",
-                    "versions.yml:md5,a1f631d2e625bc6eeba98485d6f36f3b",
                     "versions.yml:md5,f6684e4389f67f8f626c17812f368ace"
                 ]
             },
@@ -91,11 +87,6 @@
                         "bcftools": 1.22
                     }
                 },
-                {
-                    "VCF_GATHER_BCFTOOLS:TABIX_TABIX": {
-                        "tabix": 1.21
-                    }
-                },
                 {
                     "VCF_GATHER_BCFTOOLS:BCFTOOLS_SORT": {
                         "bcftools": 1.22
@@ -104,9 +95,9 @@
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
         },
-        "timestamp": "2025-09-11T14:08:26.512426"
+        "timestamp": "2025-10-28T15:17:57.172789788"
     }
 }
\ No newline at end of file