From 283cabba2f3352225a31f445dd9b1eff45dd9b46 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 09:47:03 +0100
Subject: [PATCH 01/21] tabix/tabix: update module to support region-based VCF
 extraction

---
 modules/nf-core/tabix/tabix/main.nf | 21 ++++++++++++---------
 1 file changed, 12 insertions(+), 9 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index c8bcef64eeef..3593ea16ee94 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,28 +8,31 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta), path(tab)
+    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta2), path(regions)
 
     output:
-    tuple val(meta), path("*.{tbi,csi}"), emit: index
+    tuple val(meta), path("${prefix}.vcf"), emit: vcf
     tuple val("${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
 
     script:
-    def args = task.ext.args ?: ''
+    def args        = task.ext.args   ?: ''
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def regions_arg = regions ? "-R ${regions}" : ""
     """
     tabix \\
-        --threads $task.cpus \\
-        $args \\
-        $tab
+        ${regions_arg} \\
+        ${args} \\
+        ${vcf} \\
+        > ${prefix}.vcf
 
     """
     stub:
-    def args = task.ext.args ?: ''
-    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
+    prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${tab}.${index}
+    touch ${prefix}.vcf
     """
 }

From d0071a86fc28d66fb94f7fea65cdf6452d2f7f86 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 10:04:35 +0100
Subject: [PATCH 02/21] tabix/extract: add new module for region-based VCF
 extraction

- Reverts tabix/tabix to its original indexing behaviour
- New tabix/extract module: takes a bgzipped VCF + tbi + optional regions file
- Outputs bgzipped VCF (always) and tbi index (optional, controlled by create_index input)
- Follows samtools/view pattern for optional outputs
---
 modules/nf-core/tabix/extract/environment.yml |   8 ++
 modules/nf-core/tabix/extract/main.nf         |  45 ++++++++
 modules/nf-core/tabix/extract/meta.yml        | 107 ++++++++++++++++++
 .../nf-core/tabix/extract/tests/main.nf.test  |  86 ++++++++++++++
 .../tabix/extract/tests/nextflow.config       |   6 +
 modules/nf-core/tabix/tabix/main.nf           |  21 ++--
 6 files changed, 261 insertions(+), 12 deletions(-)
 create mode 100644 modules/nf-core/tabix/extract/environment.yml
 create mode 100644 modules/nf-core/tabix/extract/main.nf
 create mode 100644 modules/nf-core/tabix/extract/meta.yml
 create mode 100644 modules/nf-core/tabix/extract/tests/main.nf.test
 create mode 100644 modules/nf-core/tabix/extract/tests/nextflow.config

diff --git a/modules/nf-core/tabix/extract/environment.yml b/modules/nf-core/tabix/extract/environment.yml
new file mode 100644
index 000000000000..771b13870781
--- /dev/null
+++ b/modules/nf-core/tabix/extract/environment.yml
@@ -0,0 +1,8 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+
+dependencies:
+  - bioconda::htslib=1.21
diff --git a/modules/nf-core/tabix/extract/main.nf b/modules/nf-core/tabix/extract/main.nf
new file mode 100644
index 000000000000..776f77dfc92a
--- /dev/null
+++ b/modules/nf-core/tabix/extract/main.nf
@@ -0,0 +1,45 @@
+process TABIX_EXTRACT {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' :
+        'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
+
+    input:
+    tuple val(meta), path(vcf), path(tbi)
+    tuple val(meta2), path(regions)
+    val create_index
+
+    output:
+    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
+    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args        = task.ext.args  ?: ''
+    def args2       = task.ext.args2 ?: ''
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def regions_arg = regions ? "-R ${regions}" : ""
+    def index_cmd   = create_index ? "tabix ${prefix}.vcf.gz" : ""
+    """
+    tabix \\
+        ${regions_arg} \\
+        ${args} \\
+        ${vcf} \\
+        | bgzip ${args2} > ${prefix}.vcf.gz
+
+    ${index_cmd}
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo "" | bgzip > ${prefix}.vcf.gz
+    ${ create_index ? "touch ${prefix}.vcf.gz.tbi" : "" }
+    """
+}
diff --git a/modules/nf-core/tabix/extract/meta.yml b/modules/nf-core/tabix/extract/meta.yml
new file mode 100644
index 000000000000..f466b831cfe2
--- /dev/null
+++ b/modules/nf-core/tabix/extract/meta.yml
@@ -0,0 +1,107 @@
+name: tabix_extract
+description: Extract regions from a bgzipped VCF file using tabix
+keywords:
+  - tabix
+  - vcf
+  - extract
+  - regions
+  - index
+tools:
+  - tabix:
+      description: |
+        Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates
+        an index file. It can also extract regions from a bgzipped VCF/BCF/BED/GFF file.
+      homepage: http://www.htslib.org/
+      documentation: http://www.htslib.org/doc/tabix.html
+      doi: 10.1093/bioinformatics/btq671
+      licence: ["MIT"]
+      identifier: biotools:tabix
+
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
+    - vcf:
+        type: file
+        description: bgzipped VCF file
+        pattern: "*.vcf.gz"
+        ontologies:
+          - edam: http://edamontology.org/format_3016 # VCF
+    - tbi:
+        type: file
+        description: Tabix index for the VCF file
+        pattern: "*.vcf.gz.tbi"
+        ontologies:
+          - edam: http://edamontology.org/format_3326 # Index
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions information
+          e.g. [ id:'regions' ]
+    - regions:
+        type: file
+        description: |
+          Optional file of regions to extract (one per line, BED or chr:start-end format).
+          Pass an empty list [] to extract all records.
+        pattern: "*.{bed,txt,tsv}"
+        ontologies: []
+  - create_index:
+      type: boolean
+      description: |
+        Whether to create a tabix index (.tbi) for the output VCF.
+        Set to true to emit the tbi output channel.
+
+output:
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - ${prefix}.vcf.gz:
+          type: file
+          description: bgzipped extracted VCF file
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3016 # VCF
+  tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - ${prefix}.vcf.gz.tbi:
+          type: file
+          description: Optional tabix index for the extracted VCF
+          pattern: "*.vcf.gz.tbi"
+          ontologies:
+            - edam: http://edamontology.org/format_3326 # Index
+  versions_tabix:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - tabix:
+          type: string
+          description: Name of the tool
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: Name of the process
+      - tabix:
+          type: string
+          description: Name of the tool
+      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
+          type: eval
+          description: The expression to obtain the version of the tool
+
+authors:
+  - "@luisasantus"
+maintainers:
+  - "@luisasantus"
diff --git a/modules/nf-core/tabix/extract/tests/main.nf.test b/modules/nf-core/tabix/extract/tests/main.nf.test
new file mode 100644
index 000000000000..3b2f36e03450
--- /dev/null
+++ b/modules/nf-core/tabix/extract/tests/main.nf.test
@@ -0,0 +1,86 @@
+nextflow_process {
+
+    name "Test Process TABIX_EXTRACT"
+    script "../main.nf"
+    process "TABIX_EXTRACT"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "tabix"
+    tag "tabix/extract"
+
+    config "./nextflow.config"
+
+    test("sarscov2 - vcf - no regions - no index") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = [ [], [] ]
+                input[2] = false
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.vcf).match("vcf_no_regions_no_index") },
+                { assert process.out.tbi == [] }
+            )
+        }
+    }
+
+    test("sarscov2 - vcf - no regions - with index") {
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = [ [], [] ]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.vcf).match("vcf_no_regions_with_index") },
+                { assert process.out.tbi.size() == 1 }
+            )
+        }
+    }
+
+    test("sarscov2 - vcf - stub") {
+        options "-stub"
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                ]
+                input[1] = [ [], [] ]
+                input[2] = true
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+}
diff --git a/modules/nf-core/tabix/extract/tests/nextflow.config b/modules/nf-core/tabix/extract/tests/nextflow.config
new file mode 100644
index 000000000000..09c4f750dce6
--- /dev/null
+++ b/modules/nf-core/tabix/extract/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: TABIX_EXTRACT {
+        ext.args = params.module_args ?: ''
+        ext.prefix = params.module_prefix ?: null
+    }
+}
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 3593ea16ee94..c8bcef64eeef 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,31 +8,28 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta), path(vcf), path(tbi)
-    tuple val(meta2), path(regions)
+    tuple val(meta), path(tab)
 
     output:
-    tuple val(meta), path("${prefix}.vcf"), emit: vcf
+    tuple val(meta), path("*.{tbi,csi}"), emit: index
     tuple val("${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
 
     script:
-    def args        = task.ext.args   ?: ''
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def regions_arg = regions ? "-R ${regions}" : ""
+    def args = task.ext.args ?: ''
     """
     tabix \\
-        ${regions_arg} \\
-        ${args} \\
-        ${vcf} \\
-        > ${prefix}.vcf
+        --threads $task.cpus \\
+        $args \\
+        $tab
 
     """
     stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
+    def args = task.ext.args ?: ''
+    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
     """
-    touch ${prefix}.vcf
+    touch ${tab}.${index}
     """
 }

From f6c4dac1d6b508dc211aac761b5e7763f0b76e30 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 10:33:24 +0100
Subject: [PATCH 03/21] tabix/extract: make both vcf and tbi outputs optional
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Always runs extraction + bgzip + tabix index. Both vcf and tbi outputs
are optional: true — callers use whichever channels they need.
---
 modules/nf-core/tabix/extract/main.nf          |  8 +++-----
 modules/nf-core/tabix/extract/meta.yml         |  6 ------
 .../nf-core/tabix/extract/tests/main.nf.test   | 18 ++++++++----------
 3 files changed, 11 insertions(+), 21 deletions(-)

diff --git a/modules/nf-core/tabix/extract/main.nf b/modules/nf-core/tabix/extract/main.nf
index 776f77dfc92a..6b09559db4d9 100644
--- a/modules/nf-core/tabix/extract/main.nf
+++ b/modules/nf-core/tabix/extract/main.nf
@@ -10,10 +10,9 @@ process TABIX_EXTRACT {
     input:
     tuple val(meta), path(vcf), path(tbi)
     tuple val(meta2), path(regions)
-    val create_index
 
     output:
-    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf
+    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf, optional: true
     tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
     tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix
 
@@ -25,7 +24,6 @@ process TABIX_EXTRACT {
     def args2       = task.ext.args2 ?: ''
     prefix          = task.ext.prefix ?: "${meta.id}"
     def regions_arg = regions ? "-R ${regions}" : ""
-    def index_cmd   = create_index ? "tabix ${prefix}.vcf.gz" : ""
     """
     tabix \\
         ${regions_arg} \\
@@ -33,13 +31,13 @@ process TABIX_EXTRACT {
         ${vcf} \\
         | bgzip ${args2} > ${prefix}.vcf.gz
 
-    ${index_cmd}
+    tabix ${prefix}.vcf.gz
     """
 
     stub:
     prefix = task.ext.prefix ?: "${meta.id}"
     """
     echo "" | bgzip > ${prefix}.vcf.gz
-    ${ create_index ? "touch ${prefix}.vcf.gz.tbi" : "" }
+    touch ${prefix}.vcf.gz.tbi
     """
 }
diff --git a/modules/nf-core/tabix/extract/meta.yml b/modules/nf-core/tabix/extract/meta.yml
index f466b831cfe2..eb0d917ecff5 100644
--- a/modules/nf-core/tabix/extract/meta.yml
+++ b/modules/nf-core/tabix/extract/meta.yml
@@ -47,12 +47,6 @@ input:
           Pass an empty list [] to extract all records.
         pattern: "*.{bed,txt,tsv}"
         ontologies: []
-  - create_index:
-      type: boolean
-      description: |
-        Whether to create a tabix index (.tbi) for the output VCF.
-        Set to true to emit the tbi output channel.
-
 output:
   vcf:
     - - meta:
diff --git a/modules/nf-core/tabix/extract/tests/main.nf.test b/modules/nf-core/tabix/extract/tests/main.nf.test
index 3b2f36e03450..b2c686f4cc32 100644
--- a/modules/nf-core/tabix/extract/tests/main.nf.test
+++ b/modules/nf-core/tabix/extract/tests/main.nf.test
@@ -11,7 +11,7 @@ nextflow_process {
 
     config "./nextflow.config"
 
-    test("sarscov2 - vcf - no regions - no index") {
+    test("sarscov2 - vcf - no regions") {
         when {
             process {
                 """
@@ -21,7 +21,6 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = [ [], [] ]
-                input[2] = false
                 """
             }
         }
@@ -29,13 +28,12 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.vcf).match("vcf_no_regions_no_index") },
-                { assert process.out.tbi == [] }
+                { assert snapshot(process.out).match() }
             )
         }
     }
 
-    test("sarscov2 - vcf - no regions - with index") {
+    test("sarscov2 - vcf - with regions") {
         when {
             process {
                 """
@@ -44,8 +42,10 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
-                input[1] = [ [], [] ]
-                input[2] = true
+                input[1] = [
+                    [ id:'regions' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                ]
                 """
             }
         }
@@ -53,8 +53,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success },
-                { assert snapshot(process.out.vcf).match("vcf_no_regions_with_index") },
-                { assert process.out.tbi.size() == 1 }
+                { assert snapshot(process.out).match() }
             )
         }
     }
@@ -70,7 +69,6 @@ nextflow_process {
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                 ]
                 input[1] = [ [], [] ]
-                input[2] = true
                 """
             }
         }

From 30ab6ea46bd5434b022693f0bd8686e3e0807f2c Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 10:39:46 +0100
Subject: [PATCH 04/21] tabix/tabix: add region extraction with optional
 vcf/tbi outputs
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

- Drop tabix/extract — functionality merged into tabix/tabix
- New input: optional regions file (pass [] to use indexing mode)
- New input: index path (required for extraction mode)
- index output: optional, emitted in indexing mode
- vcf output: optional, emitted in extraction mode
- tbi output: optional, emitted in extraction mode
---
 modules/nf-core/tabix/extract/environment.yml |   8 --
 modules/nf-core/tabix/extract/main.nf         |  43 --------
 modules/nf-core/tabix/extract/meta.yml        | 101 ------------------
 .../nf-core/tabix/extract/tests/main.nf.test  |  84 ---------------
 .../tabix/extract/tests/nextflow.config       |   6 --
 modules/nf-core/tabix/tabix/main.nf           |  54 +++++++---
 modules/nf-core/tabix/tabix/meta.yml          |  51 ++++++++-
 7 files changed, 89 insertions(+), 258 deletions(-)
 delete mode 100644 modules/nf-core/tabix/extract/environment.yml
 delete mode 100644 modules/nf-core/tabix/extract/main.nf
 delete mode 100644 modules/nf-core/tabix/extract/meta.yml
 delete mode 100644 modules/nf-core/tabix/extract/tests/main.nf.test
 delete mode 100644 modules/nf-core/tabix/extract/tests/nextflow.config

diff --git a/modules/nf-core/tabix/extract/environment.yml b/modules/nf-core/tabix/extract/environment.yml
deleted file mode 100644
index 771b13870781..000000000000
--- a/modules/nf-core/tabix/extract/environment.yml
+++ /dev/null
@@ -1,8 +0,0 @@
----
-# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-channels:
-  - conda-forge
-  - bioconda
-
-dependencies:
-  - bioconda::htslib=1.21
diff --git a/modules/nf-core/tabix/extract/main.nf b/modules/nf-core/tabix/extract/main.nf
deleted file mode 100644
index 6b09559db4d9..000000000000
--- a/modules/nf-core/tabix/extract/main.nf
+++ /dev/null
@@ -1,43 +0,0 @@
-process TABIX_EXTRACT {
-    tag "$meta.id"
-    label 'process_single'
-
-    conda "${moduleDir}/environment.yml"
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/92/92859404d861ae01afb87e2b789aebc71c0ab546397af890c7df74e4ee22c8dd/data' :
-        'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
-
-    input:
-    tuple val(meta), path(vcf), path(tbi)
-    tuple val(meta2), path(regions)
-
-    output:
-    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf, optional: true
-    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi, optional: true
-    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix
-
-    when:
-    task.ext.when == null || task.ext.when
-
-    script:
-    def args        = task.ext.args  ?: ''
-    def args2       = task.ext.args2 ?: ''
-    prefix          = task.ext.prefix ?: "${meta.id}"
-    def regions_arg = regions ? "-R ${regions}" : ""
-    """
-    tabix \\
-        ${regions_arg} \\
-        ${args} \\
-        ${vcf} \\
-        | bgzip ${args2} > ${prefix}.vcf.gz
-
-    tabix ${prefix}.vcf.gz
-    """
-
-    stub:
-    prefix = task.ext.prefix ?: "${meta.id}"
-    """
-    echo "" | bgzip > ${prefix}.vcf.gz
-    touch ${prefix}.vcf.gz.tbi
-    """
-}
diff --git a/modules/nf-core/tabix/extract/meta.yml b/modules/nf-core/tabix/extract/meta.yml
deleted file mode 100644
index eb0d917ecff5..000000000000
--- a/modules/nf-core/tabix/extract/meta.yml
+++ /dev/null
@@ -1,101 +0,0 @@
-name: tabix_extract
-description: Extract regions from a bgzipped VCF file using tabix
-keywords:
-  - tabix
-  - vcf
-  - extract
-  - regions
-  - index
-tools:
-  - tabix:
-      description: |
-        Tabix indexes a TAB-delimited genome position file in.tab.bgz and creates
-        an index file. It can also extract regions from a bgzipped VCF/BCF/BED/GFF file.
-      homepage: http://www.htslib.org/
-      documentation: http://www.htslib.org/doc/tabix.html
-      doi: 10.1093/bioinformatics/btq671
-      licence: ["MIT"]
-      identifier: biotools:tabix
-
-input:
-  - - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test' ]
-    - vcf:
-        type: file
-        description: bgzipped VCF file
-        pattern: "*.vcf.gz"
-        ontologies:
-          - edam: http://edamontology.org/format_3016 # VCF
-    - tbi:
-        type: file
-        description: Tabix index for the VCF file
-        pattern: "*.vcf.gz.tbi"
-        ontologies:
-          - edam: http://edamontology.org/format_3326 # Index
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing regions information
-          e.g. [ id:'regions' ]
-    - regions:
-        type: file
-        description: |
-          Optional file of regions to extract (one per line, BED or chr:start-end format).
-          Pass an empty list [] to extract all records.
-        pattern: "*.{bed,txt,tsv}"
-        ontologies: []
-output:
-  vcf:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test' ]
-      - ${prefix}.vcf.gz:
-          type: file
-          description: bgzipped extracted VCF file
-          pattern: "*.vcf.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3016 # VCF
-  tbi:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test' ]
-      - ${prefix}.vcf.gz.tbi:
-          type: file
-          description: Optional tabix index for the extracted VCF
-          pattern: "*.vcf.gz.tbi"
-          ontologies:
-            - edam: http://edamontology.org/format_3326 # Index
-  versions_tabix:
-    - - ${task.process}:
-          type: string
-          description: Name of the process
-      - tabix:
-          type: string
-          description: Name of the tool
-      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
-          type: eval
-          description: The expression to obtain the version of the tool
-
-topics:
-  versions:
-    - - ${task.process}:
-          type: string
-          description: Name of the process
-      - tabix:
-          type: string
-          description: Name of the tool
-      - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
-          type: eval
-          description: The expression to obtain the version of the tool
-
-authors:
-  - "@luisasantus"
-maintainers:
-  - "@luisasantus"
diff --git a/modules/nf-core/tabix/extract/tests/main.nf.test b/modules/nf-core/tabix/extract/tests/main.nf.test
deleted file mode 100644
index b2c686f4cc32..000000000000
--- a/modules/nf-core/tabix/extract/tests/main.nf.test
+++ /dev/null
@@ -1,84 +0,0 @@
-nextflow_process {
-
-    name "Test Process TABIX_EXTRACT"
-    script "../main.nf"
-    process "TABIX_EXTRACT"
-
-    tag "modules"
-    tag "modules_nfcore"
-    tag "tabix"
-    tag "tabix/extract"
-
-    config "./nextflow.config"
-
-    test("sarscov2 - vcf - no regions") {
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = [ [], [] ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 - vcf - with regions") {
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = [
-                    [ id:'regions' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
-                ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-    test("sarscov2 - vcf - stub") {
-        options "-stub"
-        when {
-            process {
-                """
-                input[0] = [
-                    [ id:'test' ],
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                ]
-                input[1] = [ [], [] ]
-                """
-            }
-        }
-
-        then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
-            )
-        }
-    }
-
-}
diff --git a/modules/nf-core/tabix/extract/tests/nextflow.config b/modules/nf-core/tabix/extract/tests/nextflow.config
deleted file mode 100644
index 09c4f750dce6..000000000000
--- a/modules/nf-core/tabix/extract/tests/nextflow.config
+++ /dev/null
@@ -1,6 +0,0 @@
-process {
-    withName: TABIX_EXTRACT {
-        ext.args = params.module_args ?: ''
-        ext.prefix = params.module_prefix ?: null
-    }
-}
diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index c8bcef64eeef..eafdeebf7749 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,28 +8,54 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta), path(tab)
+    tuple val(meta), path(tab), path(index)
+    tuple val(meta2), path(regions)
 
     output:
-    tuple val(meta), path("*.{tbi,csi}"), emit: index
-    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
+    tuple val(meta), path("*.{tbi,csi}"),  emit: index, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf,   optional: true
+    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi,   optional: true
+    tuple val("${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
 
     script:
-    def args = task.ext.args ?: ''
-    """
-    tabix \\
-        --threads $task.cpus \\
-        $args \\
-        $tab
+    def args        = task.ext.args  ?: ''
+    def args2       = task.ext.args2 ?: ''
+    prefix          = task.ext.prefix ?: "${meta.id}"
+    def regions_arg = regions ? "-R ${regions}" : ""
+    if (regions) {
+        """
+        tabix \\
+            ${regions_arg} \\
+            ${args} \\
+            ${tab} \\
+            | bgzip ${args2} > ${prefix}.vcf.gz
+
+        tabix ${prefix}.vcf.gz
+        """
+    } else {
+        """
+        tabix \\
+            --threads $task.cpus \\
+            $args \\
+            $tab
+        """
+    }
 
-    """
     stub:
     def args = task.ext.args ?: ''
-    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
-    """
-    touch ${tab}.${index}
-    """
+    prefix   = task.ext.prefix ?: "${meta.id}"
+    def idx  = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
+    if (regions) {
+        """
+        echo "" | bgzip > ${prefix}.vcf.gz
+        touch ${prefix}.vcf.gz.tbi
+        """
+    } else {
+        """
+        touch ${tab}.${idx}
+        """
+    }
 }
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index f5b6b3c1604d..ba725cddda4d 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -1,9 +1,13 @@
 name: tabix_tabix
-description: create tabix index from a sorted bgzip tab-delimited genome file
+description: |
+  Create a tabix index from a sorted bgzip TAB-delimited genome file, or
+  extract regions from a bgzipped VCF file using an optional regions file.
 keywords:
   - index
   - tabix
   - vcf
+  - extract
+  - regions
 tools:
   - tabix:
       description: Generic indexer for TAB-delimited genome position files.
@@ -23,6 +27,25 @@ input:
         description: TAB-delimited genome position file compressed with bgzip
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
         ontologies: []
+    - index:
+        type: file
+        description: |
+          Tabix index file for the input (required when using regions).
+          Pass [] when only creating an index.
+        pattern: "*.{tbi,csi}"
+        ontologies: []
+  - - meta2:
+        type: map
+        description: |
+          Groovy Map containing regions information
+          e.g. [ id:'regions' ]
+    - regions:
+        type: file
+        description: |
+          Optional file of regions to extract (BED or chr:start-end format).
+          Pass [] to create an index instead of extracting regions.
+        pattern: "*.{bed,txt,tsv}"
+        ontologies: []
 output:
   index:
     - - meta:
@@ -32,9 +55,33 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.{tbi,csi}":
           type: file
-          description: Tabix index file (either tbi or csi)
+          description: Tabix index file (tbi or csi). Emitted when no regions file is provided.
           pattern: "*.{tbi,csi}"
           ontologies: []
+  vcf:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "${prefix}.vcf.gz":
+          type: file
+          description: bgzipped VCF of extracted regions. Emitted when a regions file is provided.
+          pattern: "*.vcf.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3016 # VCF
+  tbi:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test', single_end:false ]
+      - "${prefix}.vcf.gz.tbi":
+          type: file
+          description: Tabix index for the extracted VCF. Emitted when a regions file is provided.
+          pattern: "*.vcf.gz.tbi"
+          ontologies:
+            - edam: http://edamontology.org/format_3326 # Index
   versions_tabix:
     - - ${task.process}:
           type: string

From 24f25b524da59844ba82c6fcc01bd850e3a5b778 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 14:10:02 +0100
Subject: [PATCH 05/21] add tabix/tabix

---
 modules/nf-core/tabix/tabix/main.nf           |  56 ++----
 .../nf-core/tabix/tabix/tests/main.nf.test    |  66 +++++++
 .../tabix/tabix/tests/main.nf.test.snap       | 184 ++++++++++++++++--
 3 files changed, 250 insertions(+), 56 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index eafdeebf7749..7b957fe45bce 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,54 +8,38 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta), path(tab), path(index)
+    tuple val(meta),  path(tab)
     tuple val(meta2), path(regions)
 
     output:
-    tuple val(meta), path("*.{tbi,csi}"),  emit: index, optional: true
-    tuple val(meta), path("${prefix}.vcf.gz"),     emit: vcf,   optional: true
-    tuple val(meta), path("${prefix}.vcf.gz.tbi"), emit: tbi,   optional: true
-    tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'"), topic: versions, emit: versions_tabix
+    tuple val(meta), path("*.{tbi,csi}"),   emit: index, optional: true
+    tuple val(meta), path("${prefix}.vcf"), emit: vcf,   optional: true
+    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
 
     script:
-    def args        = task.ext.args  ?: ''
-    def args2       = task.ext.args2 ?: ''
+    def args = task.ext.args ?: ''
     prefix          = task.ext.prefix ?: "${meta.id}"
     def regions_arg = regions ? "-R ${regions}" : ""
-    if (regions) {
-        """
-        tabix \\
-            ${regions_arg} \\
-            ${args} \\
-            ${tab} \\
-            | bgzip ${args2} > ${prefix}.vcf.gz
+    def output_arg  = regions ? "> ${prefix}.vcf" : ""
 
-        tabix ${prefix}.vcf.gz
-        """
-    } else {
-        """
-        tabix \\
-            --threads $task.cpus \\
-            $args \\
-            $tab
-        """
-    }
+    """
+    tabix \\
+        ${regions_arg} \\
+        --threads $task.cpus \\
+        $args \\
+        $tab \\
+        ${output_arg}
 
+    """
     stub:
     def args = task.ext.args ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
-    def idx  = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
-    if (regions) {
-        """
-        echo "" | bgzip > ${prefix}.vcf.gz
-        touch ${prefix}.vcf.gz.tbi
-        """
-    } else {
-        """
-        touch ${tab}.${idx}
-        """
-    }
+    prefix = task.ext.prefix ?: "${meta.id}"
+    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
+    """
+    touch ${tab}.${index}
+    touch ${prefix}.vcf
+    """
 }
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 19eefab87faf..f2a7bb3a0116 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -22,6 +22,7 @@ nextflow_process {
                                 [ id:'tbi_bed' ],
                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ]
                             ]
+                input[1] = [[], []]
                 """
             }
         }
@@ -45,6 +46,7 @@ nextflow_process {
                                 [ id:'tbi_gff' ],
                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ]
                             ]
+                input[1] = [[], []]
                 """
             }
         }
@@ -69,6 +71,7 @@ nextflow_process {
                                 [ id:'tbi_vcf' ],
                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
+                input[1] = [[], []]
                 """
             }
         }
@@ -93,6 +96,7 @@ nextflow_process {
                                 [ id:'vcf_csi' ],
                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
+                input[1] = [[], []]
                 """
             }
         }
@@ -106,6 +110,67 @@ nextflow_process {
 
     }
 
+    test("sarscov2_vcf_tbi_regions") {
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                                [ id:'vcf_regions' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                                ]
+                            ]
+                input[1] = [
+                                [ id:'vcf_regions' ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("sarscov2_vcf_tbi_regions_stub") {
+        options "-stub"
+        when {
+            params {
+                module_args = ''
+            }
+            process {
+                """
+                input[0] = [
+                                [ id:'vcf_regions_stub' ],
+                                [
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
+                                ]
+                            ]
+                input[1] = [
+                                [ id:'vcf_regions_stub' ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true)
+                            ]
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
     test("sarscov2_vcf_csi_stub") {
         options "-stub"
         when {
@@ -118,6 +183,7 @@ nextflow_process {
                                 [ id:'vcf_csi_stub' ],
                                 [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
                             ]
+                input[1] = [[], []]
                 """
             }
         }
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 91a3a66de0e4..6b9a5ef83f9f 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -1,4 +1,61 @@
 {
+    "sarscov2_vcf_tbi_regions_stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "vcf_regions_stub"
+                        },
+                        "test.vcf.gz.tbi.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_regions_stub"
+                        },
+                        "vcf_regions_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ],
+                "index": [
+                    [
+                        {
+                            "id": "vcf_regions_stub"
+                        },
+                        "test.vcf.gz.tbi.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "vcf_regions_stub"
+                        },
+                        "vcf_regions_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-27T13:58:12.45707",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
     "sarscov2_gff_tbi": {
         "content": [
             {
@@ -11,6 +68,9 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         "TABIX_TABIX",
                         "tabix",
@@ -25,6 +85,56 @@
                         "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
                     ]
                 ],
+                "vcf": [
+                    
+                ],
+                "versions_tabix": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ]
+            }
+        ],
+        "timestamp": "2026-03-27T14:08:24.679407",
+        "meta": {
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
+    },
+    "sarscov2_vcf_tbi_regions": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "vcf_regions"
+                        },
+                        "vcf_regions.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        "TABIX_TABIX",
+                        "tabix",
+                        "1.21"
+                    ]
+                ],
+                "index": [
+                    
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "vcf_regions"
+                        },
+                        "vcf_regions.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_TABIX",
@@ -34,11 +144,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T13:58:08.630661",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-11-20T13:47:34.055936"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2_bedgz_tbi": {
         "content": [
@@ -52,6 +162,9 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         "TABIX_TABIX",
                         "tabix",
@@ -65,6 +178,9 @@
                         },
                         "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
                     ]
+                ],
+                "vcf": [
+                    
                 ],
                 "versions_tabix": [
                     [
@@ -75,11 +191,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T14:08:20.827824",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-11-20T13:47:29.90469"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2_vcf_tbi": {
         "content": [
@@ -93,6 +209,9 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         "TABIX_TABIX",
                         "tabix",
@@ -106,6 +225,9 @@
                         },
                         "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
                     ]
+                ],
+                "vcf": [
+                    
                 ],
                 "versions_tabix": [
                     [
@@ -116,11 +238,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T14:08:28.488344",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-11-20T13:47:38.044307"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2_vcf_csi_stub": {
         "content": [
@@ -134,6 +256,14 @@
                     ]
                 ],
                 "1": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "vcf_csi_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
                     [
                         "TABIX_TABIX",
                         "tabix",
@@ -148,6 +278,14 @@
                         "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
+                "vcf": [
+                    [
+                        {
+                            "id": "vcf_csi_stub"
+                        },
+                        "vcf_csi_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
                 "versions_tabix": [
                     [
                         "TABIX_TABIX",
@@ -157,11 +295,11 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T14:08:44.196453",
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2025-12-10T14:31:29.90297082"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     },
     "sarscov2_vcf_csi": {
         "content": [
@@ -175,6 +313,9 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         "TABIX_TABIX",
                         "tabix",
@@ -188,6 +329,9 @@
                         },
                         "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
                     ]
+                ],
+                "vcf": [
+                    
                 ],
                 "versions_tabix": [
                     [
@@ -198,10 +342,10 @@
                 ]
             }
         ],
+        "timestamp": "2026-03-27T14:08:32.308038",
         "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.04.7"
-        },
-        "timestamp": "2025-11-20T13:47:42.013054"
+            "nf-test": "0.9.4",
+            "nextflow": "25.10.4"
+        }
     }
 }
\ No newline at end of file

From 39c5bd6a95d99672b8ddba41f2a28311b52d7634 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 14:25:26 +0100
Subject: [PATCH 06/21] update tests

---
 modules/nf-core/tabix/tabix/meta.yml          | 27 +++----------------
 .../nf-core/tabix/tabix/tests/main.nf.test    |  4 +--
 .../tabix/tabix/tests/main.nf.test.snap       | 14 +++++-----
 3 files changed, 13 insertions(+), 32 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index ba725cddda4d..c37098b0a421 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -24,16 +24,9 @@ input:
           e.g. [ id:'test', single_end:false ]
     - tab:
         type: file
-        description: TAB-delimited genome position file compressed with bgzip
+        description: TAB-delimited genome position file compressed with bgzip, with its index staged alongside when using regions
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
         ontologies: []
-    - index:
-        type: file
-        description: |
-          Tabix index file for the input (required when using regions).
-          Pass [] when only creating an index.
-        pattern: "*.{tbi,csi}"
-        ontologies: []
   - - meta2:
         type: map
         description: |
@@ -64,24 +57,12 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.vcf.gz":
+      - "${prefix}.vcf":
           type: file
-          description: bgzipped VCF of extracted regions. Emitted when a regions file is provided.
-          pattern: "*.vcf.gz"
+          description: Plain VCF of extracted regions. Emitted when a regions file is provided.
+          pattern: "*.vcf"
           ontologies:
             - edam: http://edamontology.org/format_3016 # VCF
-  tbi:
-    - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "${prefix}.vcf.gz.tbi":
-          type: file
-          description: Tabix index for the extracted VCF. Emitted when a regions file is provided.
-          pattern: "*.vcf.gz.tbi"
-          ontologies:
-            - edam: http://edamontology.org/format_3326 # Index
   versions_tabix:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index f2a7bb3a0116..77f01796203e 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -126,7 +126,7 @@ nextflow_process {
                             ]
                 input[1] = [
                                 [ id:'vcf_regions' ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                             ]
                 """
             }
@@ -157,7 +157,7 @@ nextflow_process {
                             ]
                 input[1] = [
                                 [ id:'vcf_regions_stub' ],
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true)
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                             ]
                 """
             }
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 6b9a5ef83f9f..3556d7f7f755 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -50,7 +50,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T13:58:12.45707",
+        "timestamp": "2026-03-27T14:24:35.528676",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -97,7 +97,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:08:24.679407",
+        "timestamp": "2026-03-27T14:24:18.982696",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -144,7 +144,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T13:58:08.630661",
+        "timestamp": "2026-03-27T14:24:31.700556",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -191,7 +191,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:08:20.827824",
+        "timestamp": "2026-03-27T14:24:15.186432",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -238,7 +238,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:08:28.488344",
+        "timestamp": "2026-03-27T14:24:22.674157",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -295,7 +295,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:08:44.196453",
+        "timestamp": "2026-03-27T14:24:39.331531",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -342,7 +342,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:08:32.308038",
+        "timestamp": "2026-03-27T14:24:27.355489",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From b54b6029fa3701d3fe2fc78a94ad215df2f880ad Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 14:45:47 +0100
Subject: [PATCH 07/21] fix test

---
 modules/nf-core/tabix/tabix/main.nf           |  8 +++--
 .../tabix/tabix/tests/main.nf.test.snap       | 32 ++++---------------
 2 files changed, 11 insertions(+), 29 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 7b957fe45bce..283633007d35 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -37,9 +37,11 @@ process TABIX_TABIX {
     stub:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
-    def index = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
+    def ext = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
+    def index = regions ? "" : "touch ${tab}.${ext}"
+    def vcf   = regions ? "touch ${prefix}.vcf" : ""
     """
-    touch ${tab}.${index}
-    touch ${prefix}.vcf
+    ${index}
+    ${vcf}
     """
 }
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 3556d7f7f755..47aaeb46465e 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -3,12 +3,7 @@
         "content": [
             {
                 "0": [
-                    [
-                        {
-                            "id": "vcf_regions_stub"
-                        },
-                        "test.vcf.gz.tbi.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "1": [
                     [
@@ -26,12 +21,7 @@
                     ]
                 ],
                 "index": [
-                    [
-                        {
-                            "id": "vcf_regions_stub"
-                        },
-                        "test.vcf.gz.tbi.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "vcf": [
                     [
@@ -50,7 +40,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:35.528676",
+        "timestamp": "2026-03-27T14:36:37.322495",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -256,12 +246,7 @@
                     ]
                 ],
                 "1": [
-                    [
-                        {
-                            "id": "vcf_csi_stub"
-                        },
-                        "vcf_csi_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "2": [
                     [
@@ -279,12 +264,7 @@
                     ]
                 ],
                 "vcf": [
-                    [
-                        {
-                            "id": "vcf_csi_stub"
-                        },
-                        "vcf_csi_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
+                    
                 ],
                 "versions_tabix": [
                     [
@@ -295,7 +275,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:39.331531",
+        "timestamp": "2026-03-27T14:36:41.192364",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From d5d6fa1559e523e7cd2f0cd4069d1fa5fdfcb9de Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 14:53:13 +0100
Subject: [PATCH 08/21] fix downstream tests

---
 modules/nf-core/tabix/tabix/tests/main.nf.test              | 2 +-
 subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf | 2 +-
 subworkflows/nf-core/vcf_extract_relate_somalier/main.nf    | 3 ++-
 subworkflows/nf-core/vcf_gather_bcftools/main.nf            | 2 +-
 4 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 77f01796203e..6ebf62be52ec 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -135,7 +135,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["vcf"])).match() }
             )
         }
     }
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
index f265df0fecf8..8c8eb40e909a 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -166,7 +166,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
         return [meta, vcf, []]
     }
 
-    TABIX_TABIX(ch_tabix_input.bgzip)
+    TABIX_TABIX(ch_tabix_input.bgzip, [[],[]])
 
     def ch_vcf_tbi = ch_tabix_input.bgzip
         .join(TABIX_TABIX.out.index, failOnDuplicate: true, failOnMismatch: true)
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
index 758b7a61a847..a196c7a20aef 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
@@ -22,7 +22,8 @@ workflow VCF_EXTRACT_RELATE_SOMALIER {
         }
 
     TABIX_TABIX(
-        ch_input.no_tbi
+        ch_input.no_tbi,
+        [[],[]]
     )
 
     ch_somalierextract_input = ch_input.no_tbi
diff --git a/subworkflows/nf-core/vcf_gather_bcftools/main.nf b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
index 0fa54ae806a4..9f871293a250 100644
--- a/subworkflows/nf-core/vcf_gather_bcftools/main.nf
+++ b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
@@ -54,7 +54,7 @@ workflow VCF_GATHER_BCFTOOLS {
         ch_tabix_input = ch_vcf_concat
     }
 
-    TABIX_TABIX(ch_tabix_input)
+    TABIX_TABIX(ch_tabix_input, [[],[]])
 
     ch_vcf_index = ch_tabix_input
         .join(TABIX_TABIX.out.index)

From 0be1e039765609118ea9bf2ea4e12576a814af65 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 15:00:26 +0100
Subject: [PATCH 09/21] update snapshot

---
 .../tabix/tabix/tests/main.nf.test.snap       | 26 +++----------------
 1 file changed, 4 insertions(+), 22 deletions(-)

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 47aaeb46465e..3d20eb4f28f8 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -87,7 +87,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:18.982696",
+        "timestamp": "2026-03-27T14:59:10.252663",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -96,24 +96,6 @@
     "sarscov2_vcf_tbi_regions": {
         "content": [
             {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "vcf_regions"
-                        },
-                        "vcf_regions.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        "TABIX_TABIX",
-                        "tabix",
-                        "1.21"
-                    ]
-                ],
                 "index": [
                     
                 ],
@@ -122,7 +104,7 @@
                         {
                             "id": "vcf_regions"
                         },
-                        "vcf_regions.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "vcf_regions.vcf"
                     ]
                 ],
                 "versions_tabix": [
@@ -134,7 +116,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:31.700556",
+        "timestamp": "2026-03-27T14:59:22.524536",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -181,7 +163,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:15.186432",
+        "timestamp": "2026-03-27T14:59:06.309394",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 44dd0197133216edacb26e2c766eb7a8101f00d9 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 17:21:24 +0100
Subject: [PATCH 10/21] add tai input for the regions

---
 modules/nf-core/tabix/tabix/main.nf           |  2 +-
 modules/nf-core/tabix/tabix/meta.yml          |  9 ++++++-
 .../nf-core/tabix/tabix/tests/main.nf.test    | 27 ++++++++++---------
 .../vcf_annotate_ensemblvep_snpeff/main.nf    |  2 +-
 .../vcf_extract_relate_somalier/main.nf       |  2 +-
 .../nf-core/vcf_gather_bcftools/main.nf       |  2 +-
 6 files changed, 26 insertions(+), 18 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 283633007d35..0fd3e43dd5ca 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,7 +8,7 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta),  path(tab)
+    tuple val(meta),  path(tab), path(tai)
     tuple val(meta2), path(regions)
 
     output:
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index c37098b0a421..f53dcd1cabc2 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -24,9 +24,16 @@ input:
           e.g. [ id:'test', single_end:false ]
     - tab:
         type: file
-        description: TAB-delimited genome position file compressed with bgzip, with its index staged alongside when using regions
+        description: TAB-delimited genome position file compressed with bgzip
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
         ontologies: []
+    - tai:
+        type: file
+        description: |
+          Tabix index for the input file. Required when extracting regions.
+          Pass [] when creating an index instead.
+        pattern: "*.{tbi,csi}"
+        ontologies: []
   - - meta2:
         type: map
         description: |
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 6ebf62be52ec..eb5f9e23b478 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -20,7 +20,8 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'tbi_bed' ],
-                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true) ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true),
+                                []
                             ]
                 input[1] = [[], []]
                 """
@@ -44,7 +45,8 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'tbi_gff' ],
-                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true) ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true),
+                                []
                             ]
                 input[1] = [[], []]
                 """
@@ -69,7 +71,8 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'tbi_vcf' ],
-                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                []
                             ]
                 input[1] = [[], []]
                 """
@@ -94,7 +97,8 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'vcf_csi' ],
-                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                []
                             ]
                 input[1] = [[], []]
                 """
@@ -119,10 +123,8 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'vcf_regions' ],
-                                [
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                                ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                             ]
                 input[1] = [
                                 [ id:'vcf_regions' ],
@@ -150,10 +152,8 @@ nextflow_process {
                 """
                 input[0] = [
                                 [ id:'vcf_regions_stub' ],
-                                [
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                                ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
                             ]
                 input[1] = [
                                 [ id:'vcf_regions_stub' ],
@@ -181,7 +181,8 @@ nextflow_process {
                 """
                 input[0] =  [
                                 [ id:'vcf_csi_stub' ],
-                                [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true) ]
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                []
                             ]
                 input[1] = [[], []]
                 """
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
index 8c8eb40e909a..863326095db9 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -166,7 +166,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
         return [meta, vcf, []]
     }
 
-    TABIX_TABIX(ch_tabix_input.bgzip, [[],[]])
+    TABIX_TABIX(ch_tabix_input.bgzip.map { meta, vcf -> [meta, vcf, []] }, [[],[]])
 
     def ch_vcf_tbi = ch_tabix_input.bgzip
         .join(TABIX_TABIX.out.index, failOnDuplicate: true, failOnMismatch: true)
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
index a196c7a20aef..1576503239c7 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
@@ -22,7 +22,7 @@ workflow VCF_EXTRACT_RELATE_SOMALIER {
         }
 
     TABIX_TABIX(
-        ch_input.no_tbi,
+        ch_input.no_tbi.map { meta, vcf -> [meta, vcf, []] },
         [[],[]]
     )
 
diff --git a/subworkflows/nf-core/vcf_gather_bcftools/main.nf b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
index 9f871293a250..7afa43492079 100644
--- a/subworkflows/nf-core/vcf_gather_bcftools/main.nf
+++ b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
@@ -54,7 +54,7 @@ workflow VCF_GATHER_BCFTOOLS {
         ch_tabix_input = ch_vcf_concat
     }
 
-    TABIX_TABIX(ch_tabix_input, [[],[]])
+    TABIX_TABIX(ch_tabix_input.map { meta, vcf -> [meta, vcf, []] }, [[],[]])
 
     ch_vcf_index = ch_tabix_input
         .join(TABIX_TABIX.out.index)

From 067bffc09bd3dd61aef664de3a907a57c691283e Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Fri, 27 Mar 2026 18:05:54 +0100
Subject: [PATCH 11/21] emit bgzipped

---
 modules/nf-core/tabix/tabix/main.nf           |  8 +++---
 modules/nf-core/tabix/tabix/meta.yml          |  6 ++---
 .../nf-core/tabix/tabix/tests/main.nf.test    |  2 +-
 .../tabix/tabix/tests/main.nf.test.snap       | 26 +++----------------
 4 files changed, 12 insertions(+), 30 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 0fd3e43dd5ca..133ac2a5841d 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -12,8 +12,8 @@ process TABIX_TABIX {
     tuple val(meta2), path(regions)
 
     output:
-    tuple val(meta), path("*.{tbi,csi}"),   emit: index, optional: true
-    tuple val(meta), path("${prefix}.vcf"), emit: vcf,   optional: true
+    tuple val(meta), path("*.{tbi,csi}"),      emit: index, optional: true
+    tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf,   optional: true
     tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
 
     when:
@@ -23,7 +23,7 @@ process TABIX_TABIX {
     def args = task.ext.args ?: ''
     prefix          = task.ext.prefix ?: "${meta.id}"
     def regions_arg = regions ? "-R ${regions}" : ""
-    def output_arg  = regions ? "> ${prefix}.vcf" : ""
+    def output_arg  = regions ? "| bgzip --threads ${task.cpus} > ${prefix}.vcf.gz" : ""
 
     """
     tabix \\
@@ -39,7 +39,7 @@ process TABIX_TABIX {
     prefix = task.ext.prefix ?: "${meta.id}"
     def ext = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
     def index = regions ? "" : "touch ${tab}.${ext}"
-    def vcf   = regions ? "touch ${prefix}.vcf" : ""
+    def vcf   = regions ? "touch ${prefix}.vcf.gz" : ""
     """
     ${index}
     ${vcf}
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index f53dcd1cabc2..ea67a57c931a 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -64,10 +64,10 @@ output:
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.vcf":
+      - "${prefix}.vcf.gz":
           type: file
-          description: Plain VCF of extracted regions. Emitted when a regions file is provided.
-          pattern: "*.vcf"
+          description: bgzipped VCF of extracted regions. Emitted when a regions file is provided.
+          pattern: "*.vcf.gz"
           ontologies:
             - edam: http://edamontology.org/format_3016 # VCF
   versions_tabix:
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index eb5f9e23b478..54fb8d87140b 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -166,7 +166,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(process.out).match() }
+                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["vcf"])).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 3d20eb4f28f8..08afa437e50b 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -2,24 +2,6 @@
     "sarscov2_vcf_tbi_regions_stub": {
         "content": [
             {
-                "0": [
-                    
-                ],
-                "1": [
-                    [
-                        {
-                            "id": "vcf_regions_stub"
-                        },
-                        "vcf_regions_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
-                    ]
-                ],
-                "2": [
-                    [
-                        "TABIX_TABIX",
-                        "tabix",
-                        "1.21"
-                    ]
-                ],
                 "index": [
                     
                 ],
@@ -28,7 +10,7 @@
                         {
                             "id": "vcf_regions_stub"
                         },
-                        "vcf_regions_stub.vcf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "vcf_regions_stub.vcf.gz"
                     ]
                 ],
                 "versions_tabix": [
@@ -40,7 +22,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:36:37.322495",
+        "timestamp": "2026-03-27T17:51:54.703596",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -104,7 +86,7 @@
                         {
                             "id": "vcf_regions"
                         },
-                        "vcf_regions.vcf"
+                        "vcf_regions.vcf.gz"
                     ]
                 ],
                 "versions_tabix": [
@@ -116,7 +98,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:59:22.524536",
+        "timestamp": "2026-03-27T17:43:18.320775",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 116bfcab61fc53277e41c37437c273369ab31952 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Mon, 30 Mar 2026 09:50:41 +0200
Subject: [PATCH 12/21] add regions to the same input channel

---
 modules/nf-core/tabix/tabix/main.nf           |  3 +--
 modules/nf-core/tabix/tabix/meta.yml          |  5 -----
 .../nf-core/tabix/tabix/tests/main.nf.test    | 20 +++++++------------
 .../vcf_annotate_ensemblvep_snpeff/main.nf    |  2 +-
 .../vcf_extract_relate_somalier/main.nf       |  3 +--
 .../nf-core/vcf_gather_bcftools/main.nf       |  2 +-
 6 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 133ac2a5841d..c3bd4d855e91 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -8,8 +8,7 @@ process TABIX_TABIX {
         'community.wave.seqera.io/library/htslib:1.21--ff8e28a189fbecaa' }"
 
     input:
-    tuple val(meta),  path(tab), path(tai)
-    tuple val(meta2), path(regions)
+    tuple val(meta),  path(tab), path(tai), path(regions)
 
     output:
     tuple val(meta), path("*.{tbi,csi}"),      emit: index, optional: true
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index ea67a57c931a..841103fcc767 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -34,11 +34,6 @@ input:
           Pass [] when creating an index instead.
         pattern: "*.{tbi,csi}"
         ontologies: []
-  - - meta2:
-        type: map
-        description: |
-          Groovy Map containing regions information
-          e.g. [ id:'regions' ]
     - regions:
         type: file
         description: |
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 54fb8d87140b..b35e6cbcc286 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -21,9 +21,9 @@ nextflow_process {
                 input[0] = [
                                 [ id:'tbi_bed' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed.gz', checkIfExists: true),
+                                [],
                                 []
                             ]
-                input[1] = [[], []]
                 """
             }
         }
@@ -46,9 +46,9 @@ nextflow_process {
                 input[0] = [
                                 [ id:'tbi_gff' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.gff3.gz', checkIfExists: true),
+                                [],
                                 []
                             ]
-                input[1] = [[], []]
                 """
             }
         }
@@ -72,9 +72,9 @@ nextflow_process {
                 input[0] =  [
                                 [ id:'tbi_vcf' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                [],
                                 []
                             ]
-                input[1] = [[], []]
                 """
             }
         }
@@ -98,9 +98,9 @@ nextflow_process {
                 input[0] =  [
                                 [ id:'vcf_csi' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                [],
                                 []
                             ]
-                input[1] = [[], []]
                 """
             }
         }
@@ -124,10 +124,7 @@ nextflow_process {
                 input[0] = [
                                 [ id:'vcf_regions' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                            ]
-                input[1] = [
-                                [ id:'vcf_regions' ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                             ]
                 """
@@ -153,10 +150,7 @@ nextflow_process {
                 input[0] = [
                                 [ id:'vcf_regions_stub' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true)
-                            ]
-                input[1] = [
-                                [ id:'vcf_regions_stub' ],
+                                file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
                             ]
                 """
@@ -182,9 +176,9 @@ nextflow_process {
                 input[0] =  [
                                 [ id:'vcf_csi_stub' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
+                                [],
                                 []
                             ]
-                input[1] = [[], []]
                 """
             }
         }
diff --git a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
index 863326095db9..3ee3fb26c75d 100644
--- a/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
+++ b/subworkflows/nf-core/vcf_annotate_ensemblvep_snpeff/main.nf
@@ -166,7 +166,7 @@ workflow VCF_ANNOTATE_ENSEMBLVEP_SNPEFF {
         return [meta, vcf, []]
     }
 
-    TABIX_TABIX(ch_tabix_input.bgzip.map { meta, vcf -> [meta, vcf, []] }, [[],[]])
+    TABIX_TABIX(ch_tabix_input.bgzip.map { meta, vcf -> [meta, vcf, [], []] })
 
     def ch_vcf_tbi = ch_tabix_input.bgzip
         .join(TABIX_TABIX.out.index, failOnDuplicate: true, failOnMismatch: true)
diff --git a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
index 1576503239c7..4b4f593c8034 100644
--- a/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
+++ b/subworkflows/nf-core/vcf_extract_relate_somalier/main.nf
@@ -22,8 +22,7 @@ workflow VCF_EXTRACT_RELATE_SOMALIER {
         }
 
     TABIX_TABIX(
-        ch_input.no_tbi.map { meta, vcf -> [meta, vcf, []] },
-        [[],[]]
+        ch_input.no_tbi.map { meta, vcf -> [meta, vcf, [], []] }
     )
 
     ch_somalierextract_input = ch_input.no_tbi
diff --git a/subworkflows/nf-core/vcf_gather_bcftools/main.nf b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
index 7afa43492079..0d0df166b65e 100644
--- a/subworkflows/nf-core/vcf_gather_bcftools/main.nf
+++ b/subworkflows/nf-core/vcf_gather_bcftools/main.nf
@@ -54,7 +54,7 @@ workflow VCF_GATHER_BCFTOOLS {
         ch_tabix_input = ch_vcf_concat
     }
 
-    TABIX_TABIX(ch_tabix_input.map { meta, vcf -> [meta, vcf, []] }, [[],[]])
+    TABIX_TABIX(ch_tabix_input.map { meta, vcf -> [meta, vcf, [], []] })
 
     ch_vcf_index = ch_tabix_input
         .join(TABIX_TABIX.out.index)

From 958601e4f40a3778fd2eedc34bf7329a360237fa Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 31 Mar 2026 10:49:41 +0200
Subject: [PATCH 13/21] Update modules/nf-core/tabix/tabix/meta.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/tabix/tabix/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index 841103fcc767..bbf38874c63c 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -27,7 +27,7 @@ input:
         description: TAB-delimited genome position file compressed with bgzip
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
         ontologies: []
-    - tai:
+    - index:
         type: file
         description: |
           Tabix index for the input file. Required when extracting regions.

From b238a9e761ba6242bcc01fec9104e537cb9add8e Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 31 Mar 2026 10:49:50 +0200
Subject: [PATCH 14/21] Update modules/nf-core/tabix/tabix/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/tabix/tabix/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index c3bd4d855e91..e8ab351e3f98 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -23,7 +23,6 @@ process TABIX_TABIX {
     prefix          = task.ext.prefix ?: "${meta.id}"
     def regions_arg = regions ? "-R ${regions}" : ""
     def output_arg  = regions ? "| bgzip --threads ${task.cpus} > ${prefix}.vcf.gz" : ""
-
     """
     tabix \\
         ${regions_arg} \\

From c8f6234d783dd167f6f317461538fc7d783f0429 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 31 Mar 2026 10:50:01 +0200
Subject: [PATCH 15/21] Update modules/nf-core/tabix/tabix/meta.yml
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/tabix/tabix/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index bbf38874c63c..6607f1b8ff29 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -61,7 +61,7 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "${prefix}.vcf.gz":
           type: file
-          description: bgzipped VCF of extracted regions. Emitted when a regions file is provided.
+          description: Bgzipped VCF of extracted regions. Emitted when a regions file is provided.
           pattern: "*.vcf.gz"
           ontologies:
             - edam: http://edamontology.org/format_3016 # VCF

From e689684d485f4fe4ce9183661d4c4701d351ac95 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 31 Mar 2026 10:50:30 +0200
Subject: [PATCH 16/21] Update modules/nf-core/tabix/tabix/main.nf
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/tabix/tabix/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index e8ab351e3f98..1af81d3ca6a8 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -37,7 +37,7 @@ process TABIX_TABIX {
     prefix = task.ext.prefix ?: "${meta.id}"
     def ext = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
     def index = regions ? "" : "touch ${tab}.${ext}"
-    def vcf   = regions ? "touch ${prefix}.vcf.gz" : ""
+    def vcf   = regions ? "echo | gzip > ${prefix}.vcf.gz" : ""
     """
     ${index}
     ${vcf}

From 349c8175b7d879c2c851ce5894e34b708acaed07 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus95@gmail.com>
Date: Tue, 31 Mar 2026 10:50:56 +0200
Subject: [PATCH 17/21] Update modules/nf-core/tabix/tabix/tests/main.nf.test
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Co-authored-by: Famke Bäuerle <45968370+famosab@users.noreply.github.com>
---
 modules/nf-core/tabix/tabix/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index b35e6cbcc286..2710289ef298 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -160,7 +160,7 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["vcf"])).match() }
+                { assert snapshot(sanitizeOutput(process.out)).match() }
             )
         }
     }

From 56846d4772b99c94e75516b8f206a84e5f0f64c2 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Tue, 31 Mar 2026 11:19:10 +0200
Subject: [PATCH 18/21] add ntf-vcf

---
 modules/nf-core/tabix/tabix/meta.yml          | 19 +++++----
 .../nf-core/tabix/tabix/tests/main.nf.test    |  8 +++-
 .../tabix/tabix/tests/main.nf.test.snap       | 41 ++++++++-----------
 3 files changed, 33 insertions(+), 35 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index 6607f1b8ff29..8226b6e96879 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -14,7 +14,8 @@ tools:
       homepage: https://www.htslib.org/doc/tabix.html
       documentation: https://www.htslib.org/doc/tabix.1.html
       doi: 10.1093/bioinformatics/btq671
-      licence: ["MIT"]
+      licence:
+        - "MIT"
       identifier: biotools:tabix
 input:
   - - meta:
@@ -27,7 +28,7 @@ input:
         description: TAB-delimited genome position file compressed with bgzip
         pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
         ontologies: []
-    - index:
+    - tai:
         type: file
         description: |
           Tabix index for the input file. Required when extracting regions.
@@ -40,7 +41,8 @@ input:
           Optional file of regions to extract (BED or chr:start-end format).
           Pass [] to create an index instead of extracting regions.
         pattern: "*.{bed,txt,tsv}"
-        ontologies: []
+        ontologies:
+          - edam: http://edamontology.org/format_3475
 output:
   index:
     - - meta:
@@ -50,7 +52,8 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "*.{tbi,csi}":
           type: file
-          description: Tabix index file (tbi or csi). Emitted when no regions file is provided.
+          description: Tabix index file (tbi or csi). Emitted when no regions file
+            is provided.
           pattern: "*.{tbi,csi}"
           ontologies: []
   vcf:
@@ -61,10 +64,12 @@ output:
             e.g. [ id:'test', single_end:false ]
       - "${prefix}.vcf.gz":
           type: file
-          description: Bgzipped VCF of extracted regions. Emitted when a regions file is provided.
+          description: Bgzipped VCF of extracted regions. Emitted when a regions
+            file is provided.
           pattern: "*.vcf.gz"
           ontologies:
-            - edam: http://edamontology.org/format_3016 # VCF
+            - edam: http://edamontology.org/format_3016
+            - edam: http://edamontology.org/format_3989
   versions_tabix:
     - - ${task.process}:
           type: string
@@ -75,7 +80,6 @@ output:
       - tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
           type: eval
           description: The expression to obtain the version of the tool
-
 topics:
   versions:
     - - ${task.process}:
@@ -87,7 +91,6 @@ topics:
       - 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/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 2710289ef298..8b00e63ef227 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -117,7 +117,7 @@ nextflow_process {
     test("sarscov2_vcf_tbi_regions") {
         when {
             params {
-                module_args = ''
+                module_args = '-h'
             }
             process {
                 """
@@ -134,7 +134,11 @@ nextflow_process {
         then {
             assertAll (
                 { assert process.success },
-                { assert snapshot(sanitizeOutput(process.out, unstableKeys: ["vcf"])).match() }
+                { assert snapshot(
+                    process.out.index,
+                    path(process.out.vcf[0][1]).vcf.getVariantsMD5(),
+                    process.out.versions_tabix
+                ).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 08afa437e50b..036e1c04cfb1 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -10,7 +10,7 @@
                         {
                             "id": "vcf_regions_stub"
                         },
-                        "vcf_regions_stub.vcf.gz"
+                        "vcf_regions_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
                 ],
                 "versions_tabix": [
@@ -22,7 +22,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T17:51:54.703596",
+        "timestamp": "2026-03-31T11:09:55.221403",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -69,7 +69,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:59:10.252663",
+        "timestamp": "2026-03-31T11:09:38.656426",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -77,28 +77,19 @@
     },
     "sarscov2_vcf_tbi_regions": {
         "content": [
-            {
-                "index": [
-                    
-                ],
-                "vcf": [
-                    [
-                        {
-                            "id": "vcf_regions"
-                        },
-                        "vcf_regions.vcf.gz"
-                    ]
-                ],
-                "versions_tabix": [
-                    [
-                        "TABIX_TABIX",
-                        "tabix",
-                        "1.21"
-                    ]
+            [
+                
+            ],
+            "d41d8cd98f00b204e9800998ecf8427e",
+            [
+                [
+                    "TABIX_TABIX",
+                    "tabix",
+                    "1.21"
                 ]
-            }
+            ]
         ],
-        "timestamp": "2026-03-27T17:43:18.320775",
+        "timestamp": "2026-03-31T11:15:49.071688",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -145,7 +136,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:59:06.309394",
+        "timestamp": "2026-03-31T11:09:34.72853",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -192,7 +183,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:22.674157",
+        "timestamp": "2026-03-31T11:09:42.627078",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 288fee06e64c81080298f173c180246d6bdb6a0f Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Tue, 31 Mar 2026 13:06:14 +0200
Subject: [PATCH 19/21] add regions

---
 modules/nf-core/tabix/tabix/tests/main.nf.test   | 12 ++++++++++--
 .../nf-core/tabix/tabix/tests/main.nf.test.snap  | 16 ++++++++--------
 2 files changed, 18 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 8b00e63ef227..1d268a3d719f 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -115,6 +115,10 @@ nextflow_process {
     }
 
     test("sarscov2_vcf_tbi_regions") {
+        setup {
+            def regions = file("${workDir}/test.regions.txt")
+            regions.text = "MT192765.1\t196\t198\nMT192765.1\t4787\t4789\n"
+        }
         when {
             params {
                 module_args = '-h'
@@ -125,7 +129,7 @@ nextflow_process {
                                 [ id:'vcf_regions' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                                file("${workDir}/test.regions.txt", checkIfExists: true)
                             ]
                 """
             }
@@ -145,6 +149,10 @@ nextflow_process {
 
     test("sarscov2_vcf_tbi_regions_stub") {
         options "-stub"
+        setup {
+            def regions = file("${workDir}/test.regions.txt")
+            regions.text = "MT192765.1\t196\t198\nMT192765.1\t4787\t4789\n"
+        }
         when {
             params {
                 module_args = ''
@@ -155,7 +163,7 @@ nextflow_process {
                                 [ id:'vcf_regions_stub' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
-                                file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/bed/test.bed', checkIfExists: true)
+                                file("${workDir}/test.regions.txt", checkIfExists: true)
                             ]
                 """
             }
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 036e1c04cfb1..a819bf30dbe8 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T11:09:55.221403",
+        "timestamp": "2026-03-31T12:50:00.816329",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -69,7 +69,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T11:09:38.656426",
+        "timestamp": "2026-03-31T12:49:41.921478",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -80,7 +80,7 @@
             [
                 
             ],
-            "d41d8cd98f00b204e9800998ecf8427e",
+            "c57539b0a39bee90f9dc6f4c60b268ed",
             [
                 [
                     "TABIX_TABIX",
@@ -89,7 +89,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-31T11:15:49.071688",
+        "timestamp": "2026-03-31T12:52:35.688937",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -136,7 +136,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T11:09:34.72853",
+        "timestamp": "2026-03-31T12:49:36.968706",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -183,7 +183,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T11:09:42.627078",
+        "timestamp": "2026-03-31T12:49:46.679693",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -230,7 +230,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:36:41.192364",
+        "timestamp": "2026-03-31T12:50:04.730679",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -277,7 +277,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-27T14:24:27.355489",
+        "timestamp": "2026-03-31T12:49:50.339466",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 54a15c239fe4fb029f9b6225650525548ae4b60e Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Tue, 31 Mar 2026 15:19:16 +0200
Subject: [PATCH 20/21] add new test

---
 modules/nf-core/tabix/tabix/tests/main.nf.test     | 12 ++----------
 .../nf-core/tabix/tabix/tests/main.nf.test.snap    | 14 +++++++-------
 2 files changed, 9 insertions(+), 17 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 1d268a3d719f..05c8279280ea 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -115,10 +115,6 @@ nextflow_process {
     }
 
     test("sarscov2_vcf_tbi_regions") {
-        setup {
-            def regions = file("${workDir}/test.regions.txt")
-            regions.text = "MT192765.1\t196\t198\nMT192765.1\t4787\t4789\n"
-        }
         when {
             params {
                 module_args = '-h'
@@ -129,7 +125,7 @@ nextflow_process {
                                 [ id:'vcf_regions' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
-                                file("${workDir}/test.regions.txt", checkIfExists: true)
+                                file('https://raw.githubusercontent.com/luisas/test-datasets/refs/heads/add-bedgraph-subset-illumina/data/genomics/sarscov2/illumina/bed/test.bed', checkIfExists: true)
                             ]
                 """
             }
@@ -149,10 +145,6 @@ nextflow_process {
 
     test("sarscov2_vcf_tbi_regions_stub") {
         options "-stub"
-        setup {
-            def regions = file("${workDir}/test.regions.txt")
-            regions.text = "MT192765.1\t196\t198\nMT192765.1\t4787\t4789\n"
-        }
         when {
             params {
                 module_args = ''
@@ -163,7 +155,7 @@ nextflow_process {
                                 [ id:'vcf_regions_stub' ],
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz', checkIfExists: true),
                                 file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/vcf/test.vcf.gz.tbi', checkIfExists: true),
-                                file("${workDir}/test.regions.txt", checkIfExists: true)
+                                file('https://raw.githubusercontent.com/luisas/test-datasets/refs/heads/add-bedgraph-subset-illumina/data/genomics/sarscov2/illumina/bed/test.bed', checkIfExists: true)
                             ]
                 """
             }
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 a819bf30dbe8..344ced64ab08 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -22,7 +22,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:50:00.816329",
+        "timestamp": "2026-03-31T14:27:49.271599",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -69,7 +69,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:49:41.921478",
+        "timestamp": "2026-03-31T14:27:32.1232",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -89,7 +89,7 @@
                 ]
             ]
         ],
-        "timestamp": "2026-03-31T12:52:35.688937",
+        "timestamp": "2026-03-31T14:38:35.804865",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -136,7 +136,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:49:36.968706",
+        "timestamp": "2026-03-31T14:27:28.328609",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -183,7 +183,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:49:46.679693",
+        "timestamp": "2026-03-31T14:27:35.800413",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -230,7 +230,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:50:04.730679",
+        "timestamp": "2026-03-31T14:27:53.111352",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -277,7 +277,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T12:49:50.339466",
+        "timestamp": "2026-03-31T14:27:39.647126",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"

From 603d2b24d581a6bdccc23a93b1dab7e49d75e298 Mon Sep 17 00:00:00 2001
From: Luisa Santus <luisa.santus@seqera.io>
Date: Wed, 1 Apr 2026 15:22:12 +0200
Subject: [PATCH 21/21] add flexible tab suffix detection

---
 modules/nf-core/tabix/tabix/main.nf           | 14 +++---
 modules/nf-core/tabix/tabix/meta.yml          | 14 +++---
 .../nf-core/tabix/tabix/tests/main.nf.test    |  2 +-
 .../tabix/tabix/tests/main.nf.test.snap       | 50 +++++++++----------
 4 files changed, 40 insertions(+), 40 deletions(-)

diff --git a/modules/nf-core/tabix/tabix/main.nf b/modules/nf-core/tabix/tabix/main.nf
index 1af81d3ca6a8..36e64c318f1a 100644
--- a/modules/nf-core/tabix/tabix/main.nf
+++ b/modules/nf-core/tabix/tabix/main.nf
@@ -11,8 +11,8 @@ process TABIX_TABIX {
     tuple val(meta),  path(tab), path(tai), path(regions)
 
     output:
-    tuple val(meta), path("*.{tbi,csi}"),      emit: index, optional: true
-    tuple val(meta), path("${prefix}.vcf.gz"), emit: vcf,   optional: true
+    tuple val(meta), path("*.{tbi,csi}"),         emit: index,     optional: true
+    tuple val(meta), path("${prefix}.*gz"),       emit: extracted, optional: true
     tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'")   , topic: versions   , emit: versions_tabix
 
     when:
@@ -21,8 +21,9 @@ process TABIX_TABIX {
     script:
     def args = task.ext.args ?: ''
     prefix          = task.ext.prefix ?: "${meta.id}"
+    def tab_suffix  = tab.name.indexOf('.') >= 0 ? tab.name.substring(tab.name.indexOf('.')) : ''
     def regions_arg = regions ? "-R ${regions}" : ""
-    def output_arg  = regions ? "| bgzip --threads ${task.cpus} > ${prefix}.vcf.gz" : ""
+    def output_arg  = regions ? "| bgzip --threads ${task.cpus} > ${prefix}${tab_suffix}" : ""
     """
     tabix \\
         ${regions_arg} \\
@@ -35,11 +36,12 @@ process TABIX_TABIX {
     stub:
     def args = task.ext.args ?: ''
     prefix = task.ext.prefix ?: "${meta.id}"
+    def tab_suffix = tab.name.indexOf('.') >= 0 ? tab.name.substring(tab.name.indexOf('.')) : ''
     def ext = args.contains("-C ") || args.contains("--csi") ? "csi" : "tbi"
-    def index = regions ? "" : "touch ${tab}.${ext}"
-    def vcf   = regions ? "echo | gzip > ${prefix}.vcf.gz" : ""
+    def index     = regions ? "" : "touch ${tab}.${ext}"
+    def extracted = regions ? "echo | gzip > ${prefix}${tab_suffix}" : ""
     """
     ${index}
-    ${vcf}
+    ${extracted}
     """
 }
diff --git a/modules/nf-core/tabix/tabix/meta.yml b/modules/nf-core/tabix/tabix/meta.yml
index 8226b6e96879..5c32b22a26bc 100644
--- a/modules/nf-core/tabix/tabix/meta.yml
+++ b/modules/nf-core/tabix/tabix/meta.yml
@@ -56,20 +56,18 @@ output:
             is provided.
           pattern: "*.{tbi,csi}"
           ontologies: []
-  vcf:
+  extracted:
     - - meta:
           type: map
           description: |
             Groovy Map containing sample information
             e.g. [ id:'test', single_end:false ]
-      - "${prefix}.vcf.gz":
+      - "${prefix}.*gz":
           type: file
-          description: Bgzipped VCF of extracted regions. Emitted when a regions
-            file is provided.
-          pattern: "*.vcf.gz"
-          ontologies:
-            - edam: http://edamontology.org/format_3016
-            - edam: http://edamontology.org/format_3989
+          description: Bgzipped file of extracted regions, preserving the input file
+            extension. Emitted when a regions file is provided.
+          pattern: "*.*gz"
+          ontologies: []
   versions_tabix:
     - - ${task.process}:
           type: string
diff --git a/modules/nf-core/tabix/tabix/tests/main.nf.test b/modules/nf-core/tabix/tabix/tests/main.nf.test
index 05c8279280ea..280eac25959d 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test
@@ -136,7 +136,7 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     process.out.index,
-                    path(process.out.vcf[0][1]).vcf.getVariantsMD5(),
+                    path(process.out.extracted[0][1]).vcf.getVariantsMD5(),
                     process.out.versions_tabix
                 ).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 344ced64ab08..27e977e0f81e 100644
--- a/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
+++ b/modules/nf-core/tabix/tabix/tests/main.nf.test.snap
@@ -2,16 +2,16 @@
     "sarscov2_vcf_tbi_regions_stub": {
         "content": [
             {
-                "index": [
-                    
-                ],
-                "vcf": [
+                "extracted": [
                     [
                         {
                             "id": "vcf_regions_stub"
                         },
                         "vcf_regions_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
                     ]
+                ],
+                "index": [
+                    
                 ],
                 "versions_tabix": [
                     [
@@ -22,7 +22,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:49.271599",
+        "timestamp": "2026-04-01T15:11:16.940666",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -48,6 +48,9 @@
                         "tabix",
                         "1.21"
                     ]
+                ],
+                "extracted": [
+                    
                 ],
                 "index": [
                     [
@@ -56,9 +59,6 @@
                         },
                         "genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
                     ]
-                ],
-                "vcf": [
-                    
                 ],
                 "versions_tabix": [
                     [
@@ -69,7 +69,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:32.1232",
+        "timestamp": "2026-04-01T15:10:57.509986",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -115,6 +115,9 @@
                         "tabix",
                         "1.21"
                     ]
+                ],
+                "extracted": [
+                    
                 ],
                 "index": [
                     [
@@ -123,9 +126,6 @@
                         },
                         "test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
                     ]
-                ],
-                "vcf": [
-                    
                 ],
                 "versions_tabix": [
                     [
@@ -136,7 +136,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:28.328609",
+        "timestamp": "2026-04-01T15:10:52.971222",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -162,6 +162,9 @@
                         "tabix",
                         "1.21"
                     ]
+                ],
+                "extracted": [
+                    
                 ],
                 "index": [
                     [
@@ -170,9 +173,6 @@
                         },
                         "test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
                     ]
-                ],
-                "vcf": [
-                    
                 ],
                 "versions_tabix": [
                     [
@@ -183,7 +183,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:35.800413",
+        "timestamp": "2026-04-01T15:11:01.818669",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -209,6 +209,9 @@
                         "tabix",
                         "1.21"
                     ]
+                ],
+                "extracted": [
+                    
                 ],
                 "index": [
                     [
@@ -217,9 +220,6 @@
                         },
                         "test.vcf.gz.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
-                ],
-                "vcf": [
-                    
                 ],
                 "versions_tabix": [
                     [
@@ -230,7 +230,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:53.111352",
+        "timestamp": "2026-04-01T15:11:22.403222",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"
@@ -256,6 +256,9 @@
                         "tabix",
                         "1.21"
                     ]
+                ],
+                "extracted": [
+                    
                 ],
                 "index": [
                     [
@@ -264,9 +267,6 @@
                         },
                         "test.vcf.gz.csi:md5,04b41c1efd9ab3c6b1e008a286e27d2b"
                     ]
-                ],
-                "vcf": [
-                    
                 ],
                 "versions_tabix": [
                     [
@@ -277,7 +277,7 @@
                 ]
             }
         ],
-        "timestamp": "2026-03-31T14:27:39.647126",
+        "timestamp": "2026-04-01T15:11:05.735059",
         "meta": {
             "nf-test": "0.9.4",
             "nextflow": "25.10.4"