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Merged
mribeirodantas merged 27 commits into from
Oct 29, 2025
Merged

adding topics channel to tabix_tabix #9267

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65feb3d
adding topics channel
mapo9 Oct 28, 2025
0e38af0
nf-test
Oct 28, 2025
31cc743
lint meta yml
Oct 28, 2025
4d4afb0
redo meta.yml
Oct 28, 2025
e301365
remove dup
Oct 28, 2025
c90452d
remove tabix version
Oct 28, 2025
58da7e8
remove tabix versions from subworkflows
Oct 28, 2025
5d60224
fix test
Oct 28, 2025
8cc8525
update snapshot
Oct 28, 2025
dee7a73
fix snapshots subworkflows
Oct 28, 2025
0d32b69
missed one subworkflow
Oct 28, 2025
363f2ab
more subworkflows
Oct 28, 2025
3087735
last (?) subworkflow
mapo9 Oct 28, 2025
b98e2af
Merge branch 'master' into tabix_fix
mapo9 Oct 28, 2025
4a96adf
Merge branch 'master' into tabix_fix
mribeirodantas Oct 28, 2025
99c0755
harshils alignmnent
mapo9 Oct 29, 2025
074b8b9
too enthusiatic when removing
mapo9 Oct 29, 2025
6382934
Merge branch 'tabix_fix' of https://github.com/mapo9/nf-core_modules …
mapo9 Oct 29, 2025
b185f5b
snaphots because bgzip versions are back
mapo9 Oct 29, 2025
0d25630
fix topics syntax for linting
mapo9 Oct 29, 2025
60d9a9f
Revert "fix topics syntax for linting"
mapo9 Oct 29, 2025
1013041
version syntax changed in test
mapo9 Oct 29, 2025
6623763
remove newline
mapo9 Oct 29, 2025
63759e0
Update modules/nf-core/tabix/tabix/main.nf
mapo9 Oct 29, 2025
ed71b74
Update modules/nf-core/tabix/tabix/meta.yml
mapo9 Oct 29, 2025
a7f4bcf
snapshot for new version_tabix name
mapo9 Oct 29, 2025
f380217
Merge branch 'topics-adoption' into tabix_fix
mribeirodantas Oct 29, 2025
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16 changes: 3 additions & 13 deletions modules/nf-core/tabix/tabix/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ process TABIX_TABIX {
tuple val(meta), path(tab)

output:
tuple val(meta), path("*.tbi"), optional:true, emit: tbi
tuple val(meta), path("*.csi"), optional:true, emit: csi
path "versions.yml" , emit: versions
tuple val(meta), path("*.tbi") , optional:true , emit: tbi
tuple val(meta), path("*.csi") , optional:true , emit: csi
tuple val("${task.process}"), val('tabix'), eval("tabix -h 2>&1 | grep -oP 'Version:\\s*\\K[^\\s]+'") , topic: versions , emit: versions1

when:
task.ext.when == null || task.ext.when
Expand All @@ -26,20 +26,10 @@ process TABIX_TABIX {
$args \\
$tab

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

stub:
"""
touch ${tab}.tbi
touch ${tab}.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
END_VERSIONS
"""
}
28 changes: 21 additions & 7 deletions modules/nf-core/tabix/tabix/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -46,13 +46,27 @@ output:
description: coordinate sorted index file
pattern: "*.{csi}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions1:
- - ${task.process}:
type: string
description: The process the versions were collected from
- tabix:
type: string
description: The tool name
- tabix -h 2>&1 | tail -1:
type: string
description: The command used to generate the version of the tool
topics:
- versions:
- - process:
type: string
description: The process the versions were collected from
- tool:
type: string
description: The tool name
- version:
type: string
description: The version of the tool
authors:
- "@joseespinosa"
- "@drpatelh"
Expand Down
17 changes: 11 additions & 6 deletions modules/nf-core/tabix/tabix/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -27,7 +27,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out,
file(process.out.tbi[0][1]).name
file(process.out.tbi[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
Expand All @@ -51,7 +52,9 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out,
file(process.out.tbi[0][1]).name).match() }
file(process.out.tbi[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}

Expand All @@ -75,7 +78,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out,
file(process.out.tbi[0][1]).name
file(process.out.tbi[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
Expand All @@ -100,7 +104,8 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out,
file(process.out.csi[0][1]).name
file(process.out.csi[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}
Expand All @@ -126,11 +131,11 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
process.out,
file(process.out.csi[0][1]).name
file(process.out.csi[0][1]).name,
process.out.findAll { key, val -> key.startsWith("versions")}
).match() }
)
}

}

}
155 changes: 120 additions & 35 deletions modules/nf-core/tabix/tabix/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,11 @@

],
"2": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
[
"TABIX_TABIX",
"tabix",
"1.21"
]
],
"csi": [

Expand All @@ -27,17 +31,30 @@
"genome.gff3.gz.tbi:md5,f79a67d95a98076e04fbe0455d825926"
]
],
"versions": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
},
"genome.gff3.gz.tbi"
"genome.gff3.gz.tbi",
{
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-03-26T13:52:48.638506004"
"timestamp": "2025-10-29T12:09:03.4031237"
},
"sarscov2_bedgz_tbi": {
"content": [
Expand All @@ -54,7 +71,11 @@

],
"2": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
[
"TABIX_TABIX",
"tabix",
"1.21"
]
],
"csi": [

Expand All @@ -67,17 +88,30 @@
"test.bed.gz.tbi:md5,9a761d51cc81835fd1199201fdbcdd5d"
]
],
"versions": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
},
"test.bed.gz.tbi"
"test.bed.gz.tbi",
{
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-03-26T13:52:44.910707349"
"timestamp": "2025-10-29T12:07:39.00957849"
},
"sarscov2_vcf_tbi": {
"content": [
Expand All @@ -94,7 +128,11 @@

],
"2": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
[
"TABIX_TABIX",
"tabix",
"1.21"
]
],
"csi": [

Expand All @@ -107,17 +145,30 @@
"test.vcf.gz.tbi:md5,d22e5b84e4fcd18792179f72e6da702e"
]
],
"versions": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
},
"test.vcf.gz.tbi"
"test.vcf.gz.tbi",
{
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-03-26T13:52:52.405662623"
"timestamp": "2025-10-29T12:09:07.979507215"
},
"sarscov2_vcf_csi_stub": {
"content": [
Expand All @@ -139,7 +190,11 @@
]
],
"2": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
[
"TABIX_TABIX",
"tabix",
"1.21"
]
],
"csi": [
[
Expand All @@ -157,17 +212,30 @@
"test.vcf.gz.tbi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
},
"test.vcf.gz.csi"
"test.vcf.gz.csi",
{
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-03-26T13:52:59.633992323"
"timestamp": "2025-10-29T12:09:17.602217734"
},
"sarscov2_vcf_csi": {
"content": [
Expand All @@ -184,7 +252,11 @@
]
],
"2": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
[
"TABIX_TABIX",
"tabix",
"1.21"
]
],
"csi": [
[
Expand All @@ -197,16 +269,29 @@
"tbi": [

],
"versions": [
"versions.yml:md5,3bfeccaff5f93fb7fca5f6dc0f0975d5"
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
},
"test.vcf.gz.csi"
"test.vcf.gz.csi",
{
"versions1": [
[
"TABIX_TABIX",
"tabix",
"1.21"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "24.10.5"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-03-26T13:52:56.083553332"
"timestamp": "2025-10-29T12:09:12.684390367"
}
}
1 change: 0 additions & 1 deletion subworkflows/nf-core/vcf_annotate_ensemblvep/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,6 @@ workflow VCF_ANNOTATE_ENSEMBLVEP {

// Gather versions of all tools used
ch_versions = ch_versions.mix(ENSEMBLVEP_VEP.out.versions)
ch_versions = ch_versions.mix(TABIX_TABIX.out.versions)

emit:
vcf_tbi = ch_vcf_tbi // channel: [ val(meta), path(vcf), path(tbi) ]
Expand Down
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