From 6b55533210f294e5825a30f03b2a649d343ad5af Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 27 Jan 2026 15:55:27 +0100
Subject: [PATCH 1/6] add topics to bgzip/tabix

---
 .../nf-core/paraphase/tests/main.nf.test.snap | 18 ++---
 modules/nf-core/tabix/bgzip/main.nf           | 10 +--
 .../tabix/bgzip/tests/main.nf.test.snap       | 80 +++++++++++++------
 .../vcf_annotate_ensemblvep_snpeff/main.nf    |  1 -
 .../tests/main.nf.test.snap                   | 20 ++---
 5 files changed, 72 insertions(+), 57 deletions(-)

diff --git a/modules/nf-core/paraphase/tests/main.nf.test.snap b/modules/nf-core/paraphase/tests/main.nf.test.snap
index 61b9c25953ef..bd34528e1658 100644
--- a/modules/nf-core/paraphase/tests/main.nf.test.snap
+++ b/modules/nf-core/paraphase/tests/main.nf.test.snap
@@ -159,10 +159,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-09-11T09:33:18.935644475"
+        "timestamp": "2026-01-27T15:17:09.630618"
     },
     "homo_sapiens - [ bam, bai ], config - csi_index": {
         "content": [
@@ -324,10 +324,10 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-09-11T09:33:01.662803887"
+        "timestamp": "2026-01-27T15:17:01.824986"
     },
     "homo_sapiens - [ bam, bai ], config": {
         "content": [
@@ -489,9 +489,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.04.6"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-09-11T09:34:24.585288444"
+        "timestamp": "2026-01-27T15:17:17.467148"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/tabix/bgzip/main.nf b/modules/nf-core/tabix/bgzip/main.nf
index c7e7462f1b5d..e80919bfd407 100644
--- a/modules/nf-core/tabix/bgzip/main.nf
+++ b/modules/nf-core/tabix/bgzip/main.nf
@@ -13,7 +13,7 @@ process TABIX_BGZIP {
     output:
     tuple val(meta), path("${output}"), emit: output
     tuple val(meta), path("*.gzi")    , emit: gzi, optional: true
-    path  "versions.yml"              , emit: versions
+    tuple val("${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
@@ -33,10 +33,6 @@ process TABIX_BGZIP {
     """
     bgzip $command -c $args -@${task.cpus} $input > ${output}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
-    END_VERSIONS
     """
 
     stub:
@@ -48,9 +44,5 @@ process TABIX_BGZIP {
     echo "" | gzip > ${output}
     touch ${output}.gzi
 
-    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/bgzip/tests/main.nf.test.snap b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
index c605d54a278c..28388109f688 100644
--- a/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
@@ -24,7 +24,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gzi": [
                     
@@ -37,16 +41,20 @@
                         "bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-03-26T13:52:19.285035543"
+        "timestamp": "2026-01-27T15:05:31.678626"
     },
     "test_stub": {
         "content": [
@@ -73,7 +81,11 @@
                     
                 ],
                 "2": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gzi": [
                     
@@ -86,16 +98,20 @@
                         "bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-03-26T13:52:15.290470496"
+        "timestamp": "2026-01-27T15:05:27.928712"
     },
     "sarscov2_vcf_bgzip_compress_gzi": {
         "content": [
@@ -117,7 +133,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gzi": [
                     [
@@ -135,16 +155,20 @@
                         "gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-03-26T13:52:26.577148245"
+        "timestamp": "2026-01-27T15:05:39.49628"
     },
     "bgzip_test": {
         "content": [
@@ -186,7 +210,11 @@
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gzi": [
                     [
@@ -204,15 +232,19 @@
                         "test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIP",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-03-26T13:52:22.850987971"
+        "timestamp": "2026-01-27T15:05:35.726067"
     }
 }
\ 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 263d02269fea..f265df0fecf8 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -119,7 +119,6 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
         TABIX_BGZIP(
             SNPEFF_SNPEFF.out.vcf
         )
-        ch_versions = ch_versions.mix(TABIX_BGZIP.out.versions.first())
 
         ch_snpeff_output = TABIX_BGZIP.out.output
     }
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 296be9d4cef7..f400e4c76403 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
@@ -143,18 +143,14 @@
                 ]
             ],
             [
-                {
-                    "VCF_ANNOTATE_ENSEMBLVEP_SNPEFF:TABIX_BGZIP": {
-                        "tabix": 1.21
-                    }
-                }
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T12:43:25.323685627"
+        "timestamp": "2026-01-27T15:42:18.478291"
     },
     "sarscov2 - ensemblvep - large chunks": {
         "content": [
@@ -297,18 +293,14 @@
                 ]
             ],
             [
-                {
-                    "VCF_ANNOTATE_ENSEMBLVEP_SNPEFF:TABIX_BGZIP": {
-                        "tabix": 1.21
-                    }
-                }
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T12:43:55.334819941"
+        "timestamp": "2026-01-27T15:43:01.336201"
     },
     "sarscov2 - ensemblvep - no scatter": {
         "content": [

From 6544c58c0adfcc5dd50d3875b5b906b7376be08e Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 27 Jan 2026 20:06:50 +0100
Subject: [PATCH 2/6] update bgzip/tabix

---
 modules/nf-core/tabix/bgziptabix/main.nf      | 12 +---
 .../tabix/bgziptabix/tests/main.nf.test.snap  | 72 +++++++++++++------
 .../nf-core/vcf_annotate_snpeff/main.nf       |  2 -
 .../tests/main.nf.test.snap                   | 19 ++---
 .../vcf_filter_bcftools_ensemblvep/main.nf    |  2 -
 .../tests/main.nf.test.snap                   | 32 +++------
 6 files changed, 68 insertions(+), 71 deletions(-)

diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index f7ff198756c7..224ed881741f 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -12,7 +12,7 @@ process TABIX_BGZIPTABIX {
 
     output:
     tuple val(meta), path("*.gz"), path("*.{tbi,csi}"), emit: gz_index
-    path  "versions.yml" ,                        emit: versions
+    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
@@ -25,11 +25,6 @@ process TABIX_BGZIPTABIX {
     bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
     tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bgzip: \$(bgzip --version | sed '1!d;s/.* //' )
-        tabix: \$(tabix --version | sed '1!d;s/.* //' )
-    END_VERSIONS
     """
 
     stub:
@@ -40,10 +35,5 @@ process TABIX_BGZIPTABIX {
     echo "" | gzip > ${prefix}.${input.getExtension()}.gz
     touch ${prefix}.${input.getExtension()}.gz.${index}
 
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        bgzip: \$(bgzip --version | sed '1!d;s/.* //' )
-        tabix: \$(tabix --version | sed '1!d;s/.* //' )
-    END_VERSIONS
     """
 }
diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
index eea9a1c0dd2b..373aa5110d02 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -12,7 +12,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gz_index": [
                     [
@@ -23,16 +27,20 @@
                         "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-11-05T16:34:13.48540422"
+        "timestamp": "2026-01-27T15:57:15.950515"
     },
     "sarscov2_bed_csi": {
         "content": [
@@ -47,7 +55,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gz_index": [
                     [
@@ -58,16 +70,20 @@
                         "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-11-05T16:34:20.086259093"
+        "timestamp": "2026-01-27T15:57:20.499666"
     },
     "sarscov2_bed_tbi_stub": {
         "content": [
@@ -82,7 +98,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gz_index": [
                     [
@@ -93,16 +113,20 @@
                         "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-11-05T16:34:33.98173417"
+        "timestamp": "2026-01-27T15:57:28.082388"
     },
     "sarscov2_bed_csi_stub": {
         "content": [
@@ -117,7 +141,11 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ],
                 "gz_index": [
                     [
@@ -128,15 +156,19 @@
                         "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,0d1392ca932108ed1febfb29a29ae919"
+                "versions_tabix": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "tabix",
+                        "1.21"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.0"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2025-11-05T16:34:26.832450064"
+        "timestamp": "2026-01-27T15:57:24.270406"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf
index 6f7ab65236f2..6dc2edec51dc 100644
--- a/subworkflows/nf-core/vcf_annotate_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_snpeff/main.nf
@@ -17,8 +17,6 @@ workflow VCF_ANNOTATE_SNPEFF {
     SNPEFF_SNPEFF(ch_vcf, val_snpeff_db, ch_snpeff_cache)
     TABIX_BGZIPTABIX(SNPEFF_SNPEFF.out.vcf)
 
-    // Gather versions of all tools used
-    ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
 
     emit:
     vcf_tbi   = TABIX_BGZIPTABIX.out.gz_index // channel: [ val(meta), path(vcf), path(tbi) ]
diff --git a/subworkflows/nf-core/vcf_annotate_snpeff/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_annotate_snpeff/tests/main.nf.test.snap
index ce7d1a4a4a89..ada9e203c020 100644
--- a/subworkflows/nf-core/vcf_annotate_snpeff/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_annotate_snpeff/tests/main.nf.test.snap
@@ -45,19 +45,14 @@
                 ]
             ],
             [
-                {
-                    "VCF_ANNOTATE_SNPEFF:TABIX_BGZIPTABIX": {
-                        "bgzip": 1.21,
-                        "tabix": 1.21
-                    }
-                }
+                
             ]
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T10:47:53.564350689"
+        "timestamp": "2026-01-27T19:42:57.855467"
     },
     "WBcel235.99 - test.vcf.gz - stub": {
         "content": [
@@ -106,7 +101,7 @@
                     ]
                 ],
                 "4": [
-                    "versions.yml:md5,c2ea3d9daa5d20fcb8a1d93021a06c93"
+                    
                 ],
                 "genes_txt": [
                     [
@@ -152,14 +147,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,c2ea3d9daa5d20fcb8a1d93021a06c93"
+                    
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T10:48:02.694171959"
+        "timestamp": "2026-01-27T19:56:34.012703"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf
index e98e54d40fbf..33b4d9a8d3f3 100644
--- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf
+++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/main.nf
@@ -39,7 +39,6 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP {
         TABIX_BGZIPTABIX(
             ENSEMBLVEP_FILTERVEP.out.output
         )
-        ch_versions = ch_versions.mix(TABIX_BGZIPTABIX.out.versions)
 
         ch_vcf = TABIX_BGZIPTABIX.out.gz_index.map { meta, vcf, _tbi -> [meta, vcf] }
         ch_tbi = TABIX_BGZIPTABIX.out.gz_index.map { meta, _vcf, tbi -> [meta, tbi] }
@@ -48,5 +47,4 @@ workflow VCF_FILTER_BCFTOOLS_ENSEMBLVEP {
     emit:
     vcf      = ch_vcf // channel: [ val(meta), path(vcf) ]
     tbi      = ch_tbi // channel: [ val(meta), path(tbi) ]
-    versions = ch_versions // channel: [ path(versions.yml) ]
 }
diff --git a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap
index 19d0c6f18807..03ac1e7b0195 100644
--- a/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap
+++ b/subworkflows/nf-core/vcf_filter_bcftools_ensemblvep/tests/main.nf.test.snap
@@ -2,12 +2,7 @@
     "vcf, hgnc_ids - filter on hgnc ids": {
         "content": [
             [
-                {
-                    "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": {
-                        "bgzip": 1.21,
-                        "tabix": 1.21
-                    }
-                }
+                
             ],
             "test.vcf.gz.tbi",
             "18e010447bd23a05a202d44daf66bcd2",
@@ -15,19 +10,14 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-07T17:55:42.872290536"
+        "timestamp": "2026-01-27T19:43:16.754963"
     },
     "vcf, hgnc_ids - filter on hgnc ids and expression": {
         "content": [
             [
-                {
-                    "VCF_FILTER_BCFTOOLS_ENSEMBLVEP:TABIX_BGZIPTABIX": {
-                        "bgzip": 1.21,
-                        "tabix": 1.21
-                    }
-                }
+                
             ],
             "test.vcf.gz.tbi",
             "18e010447bd23a05a202d44daf66bcd2",
@@ -35,9 +25,9 @@
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T12:45:00.851156984"
+        "timestamp": "2026-01-27T19:43:25.968654"
     },
     "vcf, hgnc_ids - filter on expression": {
         "content": [
@@ -73,9 +63,6 @@
                         "test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "2": [
-                    "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f"
-                ],
                 "tbi": [
                     [
                         {
@@ -91,16 +78,13 @@
                         },
                         "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
-                ],
-                "versions": [
-                    "versions.yml:md5,89322a3fc378d81d5c98da424d819f8f"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
+            "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-20T12:45:09.964268419"
+        "timestamp": "2026-01-27T19:43:35.16804"
     }
 }
\ No newline at end of file

From 15022f277e10939b4ac9983f2044f222544c9c97 Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Tue, 27 Jan 2026 20:11:52 +0100
Subject: [PATCH 3/6] update meta.yaml

---
 modules/nf-core/tabix/bgzip/meta.yml      | 28 ++++++++++++++++++-----
 modules/nf-core/tabix/bgziptabix/meta.yml | 27 +++++++++++++++++-----
 2 files changed, 43 insertions(+), 12 deletions(-)

diff --git a/modules/nf-core/tabix/bgzip/meta.yml b/modules/nf-core/tabix/bgzip/meta.yml
index 247830af7add..7b56e897cc18 100644
--- a/modules/nf-core/tabix/bgzip/meta.yml
+++ b/modules/nf-core/tabix/bgzip/meta.yml
@@ -47,13 +47,29 @@ output:
           description: Optional gzip index file for compressed inputs
           pattern: "*.gzi"
           ontologies: []
+  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 | grep -oP 'Version:\s*\K[^\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 process the versions were collected from
+      - tabix:
+          type: string
+          description: The tool name
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
 authors:
   - "@joseespinosa"
   - "@drpatelh"
diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
index 82ce84e2c0dc..f9d91b33bcec 100644
--- a/modules/nf-core/tabix/bgziptabix/meta.yml
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -42,13 +42,28 @@ output:
           description: Tabix index file (either tbi or csi)
           pattern: "*.{tbi,csi}"
           ontologies: []
+  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 | grep -oP 'Version:\s*\K[^\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 process the versions were collected from
+      - tabix:
+          type: string
+          description: The tool name
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@maxulysse"
   - "@DLBPointon"

From 56d08a4af736894aa644764298f20692f8e1235c Mon Sep 17 00:00:00 2001
From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 29 Jan 2026 16:54:49 +0100
Subject: [PATCH 4/6] update topics

---
 modules/nf-core/tabix/bgziptabix/main.nf  |  1 +
 modules/nf-core/tabix/bgziptabix/meta.yml | 19 +++++++++++++++++++
 2 files changed, 20 insertions(+)

diff --git a/modules/nf-core/tabix/bgziptabix/main.nf b/modules/nf-core/tabix/bgziptabix/main.nf
index 224ed881741f..30eae745fc7c 100644
--- a/modules/nf-core/tabix/bgziptabix/main.nf
+++ b/modules/nf-core/tabix/bgziptabix/main.nf
@@ -13,6 +13,7 @@ process TABIX_BGZIPTABIX {
     output:
     tuple val(meta), path("*.gz"), path("*.{tbi,csi}"), emit: gz_index
     tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
+    tuple val("${task.process}"), val('bgzip'), eval("bgzip --version | sed '1!d;s/.* //'"), topic: versions, emit: versions_bgzip
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
index f9d91b33bcec..333816dde46f 100644
--- a/modules/nf-core/tabix/bgziptabix/meta.yml
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -52,6 +52,16 @@ output:
       - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
           type: eval
           description: The expression to obtain the version of the tool
+  versions_bgzip:
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bgzip:
+          type: string
+          description: The tool name
+      - bgzip -h 2>&1 | sed 's/^.*Version: //;s/Usage:.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
 
 topics:
   versions:
@@ -64,6 +74,15 @@ topics:
       - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
           type: eval
           description: The expression to obtain the version of the tool
+    - - ${task.process}:
+          type: string
+          description: The process the versions were collected from
+      - bgzip:
+          type: string
+          description: The tool name
+      - bgzip -h 2>&1 | sed 's/^.*Version: //;s/Usage:.*//':
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@maxulysse"
   - "@DLBPointon"

From 4ece54bf5906472cc1927aa5d9cc71e1a3976592 Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 29 Jan 2026 23:23:13 +0100
Subject: [PATCH 5/6] update meta.yaml

---
 modules/nf-core/tabix/bgziptabix/meta.yml | 8 +++++---
 1 file changed, 5 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/tabix/bgziptabix/meta.yml b/modules/nf-core/tabix/bgziptabix/meta.yml
index 333816dde46f..2a3078c55faa 100644
--- a/modules/nf-core/tabix/bgziptabix/meta.yml
+++ b/modules/nf-core/tabix/bgziptabix/meta.yml
@@ -1,5 +1,6 @@
 name: tabix_bgziptabix
-description: bgzip a sorted tab-delimited genome file and then create tabix index
+description: bgzip a sorted tab-delimited genome file and then create tabix
+  index
 keywords:
   - bgzip
   - compress
@@ -59,7 +60,7 @@ output:
       - bgzip:
           type: string
           description: The tool name
-      - bgzip -h 2>&1 | sed 's/^.*Version: //;s/Usage:.*//':
+      - bgzip --version | sed '1!d;s/.* //':
           type: eval
           description: The expression to obtain the version of the tool
 
@@ -80,9 +81,10 @@ topics:
       - bgzip:
           type: string
           description: The tool name
-      - bgzip -h 2>&1 | sed 's/^.*Version: //;s/Usage:.*//':
+      - bgzip --version | sed '1!d;s/.* //':
           type: eval
           description: The expression to obtain the version of the tool
+
 authors:
   - "@maxulysse"
   - "@DLBPointon"

From 053ee0823368ef67ba456a924c175a7bed94277c Mon Sep 17 00:00:00 2001
From: ramprasadn <20065894+ramprasadn@users.noreply.github.com>
Date: Thu, 29 Jan 2026 23:40:14 +0100
Subject: [PATCH 6/6] update snaps

---
 .../tabix/bgziptabix/tests/main.nf.test.snap  | 64 +++++++++++++++++--
 1 file changed, 60 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
index 373aa5110d02..cf3ce8aa8c4e 100644
--- a/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/bgziptabix/tests/main.nf.test.snap
@@ -18,6 +18,13 @@
                         "1.21"
                     ]
                 ],
+                "2": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "gz_index": [
                     [
                         {
@@ -27,6 +34,13 @@
                         "tbi_test.bed.gz.tbi:md5,ca06caf88b1e3c67d5fcba0a1460b52c"
                     ]
                 ],
+                "versions_bgzip": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_BGZIPTABIX",
@@ -40,7 +54,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-27T15:57:15.950515"
+        "timestamp": "2026-01-29T23:36:32.823417"
     },
     "sarscov2_bed_csi": {
         "content": [
@@ -61,6 +75,13 @@
                         "1.21"
                     ]
                 ],
+                "2": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "gz_index": [
                     [
                         {
@@ -70,6 +91,13 @@
                         "csi_test.bed.gz.csi:md5,c9c0377de58fdc89672bb3005a0d69f5"
                     ]
                 ],
+                "versions_bgzip": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_BGZIPTABIX",
@@ -83,7 +111,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-27T15:57:20.499666"
+        "timestamp": "2026-01-29T23:36:36.715208"
     },
     "sarscov2_bed_tbi_stub": {
         "content": [
@@ -104,6 +132,13 @@
                         "1.21"
                     ]
                 ],
+                "2": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "gz_index": [
                     [
                         {
@@ -113,6 +148,13 @@
                         "test.bed.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "versions_bgzip": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_BGZIPTABIX",
@@ -126,7 +168,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-27T15:57:28.082388"
+        "timestamp": "2026-01-29T23:36:45.016007"
     },
     "sarscov2_bed_csi_stub": {
         "content": [
@@ -147,6 +189,13 @@
                         "1.21"
                     ]
                 ],
+                "2": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "gz_index": [
                     [
                         {
@@ -156,6 +205,13 @@
                         "test.bed.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "versions_bgzip": [
+                    [
+                        "TABIX_BGZIPTABIX",
+                        "bgzip",
+                        "1.21"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_BGZIPTABIX",
@@ -169,6 +225,6 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.3"
         },
-        "timestamp": "2026-01-27T15:57:24.270406"
+        "timestamp": "2026-01-29T23:36:40.5401"
     }
 }
\ No newline at end of file