Skip to content

Add topics channel to tabix/bgzip and tabix/bgziptabix #9790

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
ramprasadn wants to merge 3 commits into
base: master
Choose a base branch
from
+183 −140
Open

Add topics channel to tabix/bgzip and tabix/bgziptabix #9790

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
3 commits
Select commit Hold shift + click to select a range
6b55533
add topics to bgzip/tabix
ramprasadn Jan 27, 2026
6544c58
update bgzip/tabix
ramprasadn Jan 27, 2026
15022f2
update meta.yaml
ramprasadn Jan 27, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 9 additions & 9 deletions modules/nf-core/paraphase/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -159,10 +159,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-09-11T09:33:18.935644475"
"timestamp": "2026-01-27T15:17:09.630618"
},
"homo_sapiens - [ bam, bai ], config - csi_index": {
"content": [
Expand Down Expand Up @@ -324,10 +324,10 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-09-11T09:33:01.662803887"
"timestamp": "2026-01-27T15:17:01.824986"
},
"homo_sapiens - [ bam, bai ], config": {
"content": [
Expand Down Expand Up @@ -489,9 +489,9 @@
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-09-11T09:34:24.585288444"
"timestamp": "2026-01-27T15:17:17.467148"
}
}
10 changes: 1 addition & 9 deletions modules/nf-core/tabix/bgzip/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process TABIX_BGZIP {
output:
tuple val(meta), path("${output}"), emit: output
tuple val(meta), path("*.gzi") , emit: gzi, optional: true
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix

when:
task.ext.when == null || task.ext.when
Expand All @@ -33,10 +33,6 @@ process TABIX_BGZIP {
"""
bgzip $command -c $args -@${task.cpus} $input > ${output}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""

stub:
Expand All @@ -48,9 +44,5 @@ process TABIX_BGZIP {
echo "" | gzip > ${output}
touch ${output}.gzi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
28 changes: 22 additions & 6 deletions modules/nf-core/tabix/bgzip/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -47,13 +47,29 @@ output:
description: Optional gzip index file for compressed inputs
pattern: "*.gzi"
ontologies: []
versions_tabix:
- - ${task.process}:
type: string
description: The process the versions were collected from
- tabix:
type: string
description: The tool name
- tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The process the versions were collected from
- tabix:
type: string
description: The tool name
- tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@joseespinosa"
- "@drpatelh"
Expand Down
80 changes: 56 additions & 24 deletions modules/nf-core/tabix/bgzip/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -24,7 +24,11 @@

],
"2": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
],
"gzi": [

Expand All @@ -37,16 +41,20 @@
"bedgz_test.bed:md5,87a15eb9c2ff20ccd5cd8735a28708f7"
]
],
"versions": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
"versions_tabix": [
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T13:52:19.285035543"
"timestamp": "2026-01-27T15:05:31.678626"
},
"test_stub": {
"content": [
Expand All @@ -73,7 +81,11 @@

],
"2": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
],
"gzi": [

Expand All @@ -86,16 +98,20 @@
"bgzip_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
]
],
"versions": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
"versions_tabix": [
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T13:52:15.290470496"
"timestamp": "2026-01-27T15:05:27.928712"
},
"sarscov2_vcf_bgzip_compress_gzi": {
"content": [
Expand All @@ -117,7 +133,11 @@
]
],
"2": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
],
"gzi": [
[
Expand All @@ -135,16 +155,20 @@
"gzi_compress_test.vcf.gz:md5,8e722884ffb75155212a3fc053918766"
]
],
"versions": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
"versions_tabix": [
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T13:52:26.577148245"
"timestamp": "2026-01-27T15:05:39.49628"
},
"bgzip_test": {
"content": [
Expand Down Expand Up @@ -186,7 +210,11 @@
]
],
"2": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
],
"gzi": [
[
Expand All @@ -204,15 +232,19 @@
"test_stub.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,8721da9158d25c69b2215adf9cdc9fde"
"versions_tabix": [
[
"TABIX_BGZIP",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.3"
},
"timestamp": "2025-03-26T13:52:22.850987971"
"timestamp": "2026-01-27T15:05:35.726067"
}
}
12 changes: 1 addition & 11 deletions modules/nf-core/tabix/bgziptabix/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ process TABIX_BGZIPTABIX {

output:
tuple val(meta), path("*.gz"), path("*.{tbi,csi}"), emit: gz_index
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions_tabix

when:
task.ext.when == null || task.ext.when
Expand All @@ -25,11 +25,6 @@ process TABIX_BGZIPTABIX {
bgzip --threads ${task.cpus} -c $args $input > ${prefix}.${input.getExtension()}.gz
tabix --threads ${task.cpus} $args2 ${prefix}.${input.getExtension()}.gz
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bgzip: \$(bgzip --version | sed '1!d;s/.* //' )
tabix: \$(tabix --version | sed '1!d;s/.* //' )
END_VERSIONS
"""

stub:
Expand All @@ -40,10 +35,5 @@ process TABIX_BGZIPTABIX {
echo "" | gzip > ${prefix}.${input.getExtension()}.gz
touch ${prefix}.${input.getExtension()}.gz.${index}
cat <<-END_VERSIONS > versions.yml
"${task.process}":
bgzip: \$(bgzip --version | sed '1!d;s/.* //' )
tabix: \$(tabix --version | sed '1!d;s/.* //' )
END_VERSIONS
"""
}
27 changes: 21 additions & 6 deletions modules/nf-core/tabix/bgziptabix/meta.yml
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -42,13 +42,28 @@ output:
description: Tabix index file (either tbi or csi)
pattern: "*.{tbi,csi}"
ontologies: []
versions_tabix:
- - ${task.process}:
type: string
description: The process the versions were collected from
- tabix:
type: string
description: The tool name
- tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
type: eval
description: The expression to obtain the version of the tool

topics:
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
- - ${task.process}:
type: string
description: The process the versions were collected from
- tabix:
type: string
description: The tool name
- tabix -h 2>&1 | grep -oP 'Version:\s*\K[^\s]+':
type: eval
description: The expression to obtain the version of the tool
authors:
- "@maxulysse"
- "@DLBPointon"
Expand Down
Loading
Loading