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Update samtools/index to version topic #9613

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2abe099
Update samtools/index to version topic
SPPearce Dec 31, 2025
e2d8da9
Merge branch 'master' into samtools_index_topic
SPPearce Jan 5, 2026
d97075b
Update snapshots
SPPearce Jan 6, 2026
a861ca4
Merge remote-tracking branch 'origin/master' into samtools_index_topic
SPPearce Jan 6, 2026
062b4ce
Swap more swfs to nft-bam
SPPearce Jan 6, 2026
3262b3d
Update more snapshots
SPPearce Jan 6, 2026
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12 changes: 1 addition & 11 deletions modules/nf-core/samtools/index/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -14,7 +14,7 @@ process SAMTOOLS_INDEX {
tuple val(meta), path("*.bai") , optional:true, emit: bai
tuple val(meta), path("*.csi") , optional:true, emit: csi
tuple val(meta), path("*.crai"), optional:true, emit: crai
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('samtools'), eval("samtools version | sed '1!d;s/.* //'"), topic: versions, emit: versions_samtools

when:
task.ext.when == null || task.ext.when
Expand All @@ -27,11 +27,6 @@ process SAMTOOLS_INDEX {
-@ ${task.cpus} \\
$args \\
$input

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

stub:
Expand All @@ -40,10 +35,5 @@ process SAMTOOLS_INDEX {
"crai" : args.contains("-c") ? "csi" : "bai"
"""
touch ${input}.${extension}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
28 changes: 22 additions & 6 deletions modules/nf-core/samtools/index/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -60,13 +60,29 @@ output:
description: BAM/CRAM/SAM index file
pattern: "*.{bai,crai,sai}"
ontologies: []
versions_samtools:
- - ${task.process}:
type: string
description: The process the versions were collected from
- samtools:
type: string
description: The tool name
- "samtools version | sed '1!d;s/.* //'":
type: string
description: The command used to generate 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
- samtools:
type: string
description: The tool name
- "samtools version | sed '1!d;s/.* //'":
type: string
description: The command used to generate the version of the tool

authors:
- "@drpatelh"
- "@ewels"
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/samtools/index/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -67,7 +67,7 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
file(process.out.csi[0][1]).name,
process.out.versions
process.out.findAll { key, val -> key.startsWith("versions") }
).match() }
)
}
Expand Down
118 changes: 82 additions & 36 deletions modules/nf-core/samtools/index/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -18,7 +18,11 @@

],
"3": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
],
"bai": [

Expand All @@ -35,16 +39,20 @@
"test.paired_end.sorted.bam.csi:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:38.25787"
"timestamp": "2025-12-31T15:25:32.706640639"
},
"crai - stub": {
"content": [
Expand All @@ -65,7 +73,11 @@
]
],
"3": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
],
"bai": [

Expand All @@ -82,16 +94,20 @@
"csi": [

],
"versions": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:34.496412"
"timestamp": "2025-12-31T15:25:24.477945713"
},
"bai - stub": {
"content": [
Expand All @@ -112,7 +128,11 @@

],
"3": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
],
"bai": [
[
Expand All @@ -129,29 +149,39 @@
"csi": [

],
"versions": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:25.934431"
"timestamp": "2025-12-31T15:25:16.221396835"
},
"csi": {
"content": [
"test.paired_end.sorted.bam.csi",
[
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
]
{
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:22.262088"
"timestamp": "2025-12-31T15:25:08.621945161"
},
"crai": {
"content": [
Expand All @@ -172,7 +202,11 @@
]
],
"3": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
],
"bai": [

Expand All @@ -189,16 +223,20 @@
"csi": [

],
"versions": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:18.191664"
"timestamp": "2025-12-31T15:25:01.071934898"
},
"bai": {
"content": [
Expand All @@ -219,7 +257,11 @@

],
"3": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
],
"bai": [
[
Expand All @@ -236,15 +278,19 @@
"csi": [

],
"versions": [
"versions.yml:md5,b8717818c91b07de87c2a5590bad02e6"
"versions_samtools": [
[
"SAMTOOLS_INDEX",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:13:08.51539"
"timestamp": "2025-12-31T15:24:52.105615274"
}
}
4 changes: 2 additions & 2 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE {

main:

ch_versions = Channel.empty()
ch_versions = channel.empty()

//
// umicollapse in bam mode (thus hardcode mode input channel to 'bam')
Expand All @@ -24,7 +24,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMICOLLAPSE {
// Index BAM file and run samtools stats, flagstat and idxstats
//
SAMTOOLS_INDEX ( UMICOLLAPSE.out.bam )
ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
// SAMTOOLS_INDEX emits version as a topic channel
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@maxulysse maxulysse Jan 8, 2026

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Suggested change
// SAMTOOLS_INDEX emits version as a topic channel

I usually just delete the whole line

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@SPPearce SPPearce Jan 8, 2026

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Yeah, I've been doing this, to make it clearer while we still have mixed subworkflows.


ch_bam_bai_dedup = UMICOLLAPSE.out.bam
.join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
Expand Down
7 changes: 3 additions & 4 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umicollapse/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -21,15 +21,14 @@
[
"versions.yml:md5,15a99b83c8965f9b29d0e9e6dbdef621",
"versions.yml:md5,61bd927f2f2121e34d94692a62305955",
"versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
"versions.yml:md5,71d8ff70a0f65311659c446278f10b1a"
"versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-01T02:35:06.350407"
"timestamp": "2025-12-31T15:30:53.374645362"
},
"test_bam_dedup_stats_samtools_umicollapse_flagstats": {
"content": [
Expand Down
2 changes: 1 addition & 1 deletion subworkflows/nf-core/bam_dedup_stats_samtools_umitools/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -25,7 +25,7 @@ workflow BAM_DEDUP_STATS_SAMTOOLS_UMITOOLS {
// Index BAM file and run samtools stats, flagstat and idxstats
//
SAMTOOLS_INDEX ( UMITOOLS_DEDUP.out.bam )
ch_versions = ch_versions.mix(SAMTOOLS_INDEX.out.versions.first())
// SAMTOOLS_INDEX emits version as a topic channel

ch_bam_bai_dedup = UMITOOLS_DEDUP.out.bam
.join(SAMTOOLS_INDEX.out.bai, by: [0], remainder: true)
Expand Down
17 changes: 7 additions & 10 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -29,15 +29,14 @@
[
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-01T02:35:42.524116"
"timestamp": "2025-12-31T15:28:36.488926399"
},
"sarscov2_bam_bai - stub": {
"content": [
Expand Down Expand Up @@ -96,8 +95,7 @@
"7": [
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45"
],
"bai": [
[
Expand Down Expand Up @@ -153,15 +151,14 @@
"versions": [
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45"
]
}
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.0"
"nextflow": "25.10.2"
},
"timestamp": "2025-11-01T02:35:58.59434"
"timestamp": "2025-12-31T15:28:52.020714406"
}
}
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