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feat: update samtools stats module with version topic support #9330

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Merged
merged 11 commits into from
Nov 4, 2025
+177 −199
Merged

feat: update samtools stats module with version topic support #9330

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e8ded25
Adds version topic channel to SAMTOOLS_STATS
mribeirodantas Nov 1, 2025
6ada243
Removes version mix in subworkflow
mribeirodantas Nov 1, 2025
86949d5
Removes version mix for samtools sort
mribeirodantas Nov 1, 2025
4ce38ee
Updates snapshots for tests
mribeirodantas Nov 1, 2025
f1612eb
Update modules/nf-core/samtools/stats/main.nf
mribeirodantas Nov 2, 2025
61ed8fb
Update modules/nf-core/samtools/stats/meta.yml
mribeirodantas Nov 2, 2025
f0895e3
Fixes meta.yml
mribeirodantas Nov 3, 2025
71e5f1e
[automated] Update gpu snapshot
nf-core-bot Nov 3, 2025
5bf41bd
[automated] Update gpu snapshot
nf-core-bot Nov 3, 2025
b288aa3
remove accidentally added file
mashehu Nov 3, 2025
b3965c3
Merge branch 'addtopicversion_samtoolsstats' of github.com:nf-core/mo…
mashehu Nov 3, 2025
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14 changes: 2 additions & 12 deletions modules/nf-core/samtools/stats/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,8 +13,8 @@ process SAMTOOLS_STATS {

output:
tuple val(meta), path("*.stats"), emit: stats
path "versions.yml" , emit: versions

tuple val("${task.process}"), val('samtools'), eval('samtools --version | head -1 | sed -e "s/samtools //"'), emit: versions_samtools, topic: versions
when:
task.ext.when == null || task.ext.when

Expand All @@ -28,21 +28,11 @@ process SAMTOOLS_STATS {
${reference} \\
${input} \\
> ${prefix}.stats

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

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
"""
touch ${prefix}.stats

cat <<-END_VERSIONS > versions.yml
"${task.process}":
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
29 changes: 22 additions & 7 deletions modules/nf-core/samtools/stats/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,13 +55,28 @@ output:
description: File containing samtools stats output
pattern: "*.{stats}"
ontologies: []
versions:
- versions.yml:
type: file
description: File containing software versions
pattern: "versions.yml"
ontologies:
- edam: http://edamontology.org/format_3750 # YAML
versions_samtools:
- - ${task.process}:
type: string
description: Name of the process
- samtools:
type: string
description: Name of the tool
- samtools --version | head -1 | sed -e "s/samtools //:
type: string
description: Version of samtools used

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:
- "@drpatelh"
- "@FriederikeHanssen"
Expand Down
80 changes: 56 additions & 24 deletions modules/nf-core/samtools/stats/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -12,7 +12,11 @@
]
],
"1": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
],
"stats": [
[
Expand All @@ -23,16 +27,20 @@
"test.stats:md5,f4aec6c41b73d34ac2fc6b3253aa39ba"
]
],
"versions": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
"versions_samtools": [
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-10T15:05:52.878044"
"timestamp": "2025-11-01T02:27:18.460724"
},
"bam - stub": {
"content": [
Expand All @@ -47,7 +55,11 @@
]
],
"1": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
],
"stats": [
[
Expand All @@ -58,16 +70,20 @@
"test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
"versions_samtools": [
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-10T15:05:56.722672"
"timestamp": "2025-11-01T02:27:30.245839"
},
"cram - stub": {
"content": [
Expand All @@ -82,7 +98,11 @@
]
],
"1": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
],
"stats": [
[
Expand All @@ -93,16 +113,20 @@
"test.stats:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
"versions_samtools": [
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-10T15:06:13.766719"
"timestamp": "2025-11-01T02:27:39.041649"
},
"bam": {
"content": [
Expand All @@ -117,7 +141,11 @@
]
],
"1": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
],
"stats": [
[
Expand All @@ -128,15 +156,19 @@
"test.stats:md5,41ba8ad30ddb598dadb177a54c222ab9"
]
],
"versions": [
"versions.yml:md5,7668882f411d0f6356f14a1b8b56fa3c"
"versions_samtools": [
[
"SAMTOOLS_STATS",
"samtools",
"1.22.1"
]
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-10T15:05:30.301153"
"timestamp": "2025-11-01T02:26:55.988241"
}
}
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 @@ -22,15 +22,14 @@
"versions.yml:md5,15a99b83c8965f9b29d0e9e6dbdef621",
"versions.yml:md5,61bd927f2f2121e34d94692a62305955",
"versions.yml:md5,657bce03545b4c57f9c5fc4314bf85f7",
"versions.yml:md5,67313fdb9b1b2ccee1c00408cc7ae072",
"versions.yml:md5,71d8ff70a0f65311659c446278f10b1a"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-10T13:32:36.702719"
"timestamp": "2025-11-01T02:35:06.350407"
},
"test_bam_dedup_stats_samtools_umicollapse_flagstats": {
"content": [
Expand Down
19 changes: 8 additions & 11 deletions subworkflows/nf-core/bam_dedup_stats_samtools_umitools/tests/main.nf.test.snap
View file
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Original file line number Diff line number Diff line change
Expand Up @@ -28,17 +28,16 @@
],
[
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-11T09:42:03.400348"
"timestamp": "2025-11-01T02:35:42.524116"
},
"sarscov2_bam_bai - stub": {
"content": [
Expand Down Expand Up @@ -83,7 +82,7 @@
{
"id": "test"
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"6": [
Expand All @@ -96,7 +95,6 @@
],
"7": [
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
Expand Down Expand Up @@ -133,7 +131,7 @@
{
"id": "test"
},
"test.flagstat:md5,d41d8cd98f00b204e9800998ecf8427e"
"test.flagstat:md5,67394650dbae96d1a4fcc70484822159"
]
],
"idxstats": [
Expand All @@ -154,17 +152,16 @@
],
"versions": [
"versions.yml:md5,0ebfc47a75bd075329a7434161100f8f",
"versions.yml:md5,8170256bdee0615a3a9c3ad9f44c99d7",
"versions.yml:md5,a8989d3d3bf9dde36a1d0664e54fccb5",
"versions.yml:md5,c4d5d9b171cc7b206cb14f7043f16e45",
"versions.yml:md5,e687e4e909255370121fcbec5a4299d1"
]
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.0"
},
"timestamp": "2025-09-11T09:42:13.338671"
"timestamp": "2025-11-01T02:35:58.59434"
}
}
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