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Varscan topic #12038

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ec1237d
Swap umitools/group to topics
SPPearce Jun 17, 2026
822e663
umitools/group to topic
SPPearce Jun 18, 2026
7fac9ea
Swap to use same version extraction as other submodules
SPPearce Jun 18, 2026
b7f4a3a
Fix
SPPearce Jun 18, 2026
817b461
Swap varscan to topics
SPPearce Jun 18, 2026
4ae404a
Remove massive indent
SPPearce Jun 18, 2026
d5905de
Merge branch 'master' into varscan_topic
SPPearce Jun 18, 2026
3fc4112
Fix version extraction
SPPearce Jun 18, 2026
12b97c0
Add edam comments back
SPPearce Jun 18, 2026
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4 changes: 2 additions & 2 deletions modules/nf-core/umitools/group/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,13 +5,13 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/umi_tools
- bioconda::pysam=0.22.0
- bioconda::umi_tools=1.1.6
- conda-forge::future=0.18.3
- conda-forge::matplotlib=3.8.2
- conda-forge::numpy=1.26.4
- conda-forge::pandas=2.2.0
- conda-forge::pybktree=1.1
- conda-forge::python=3.9.18
- conda-forge::regex=2023.12.25
- conda-forge::scipy=1.12.0
- conda-forge::pybktree=1.1
- bioconda::pysam=0.22.0
12 changes: 1 addition & 11 deletions modules/nf-core/umitools/group/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -16,7 +16,7 @@ process UMITOOLS_GROUP {
tuple val(meta), path("*.log") , emit: log
tuple val(meta), path("${prefix}.bam"), optional: true, emit: bam
tuple val(meta), path("*.tsv") , optional: true, emit: tsv
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('umitools'), eval("umi_tools --version | sed 's/UMI-tools version: //'"), emit: versions_umitools, topic: versions

when:
task.ext.when == null || task.ext.when
Expand All @@ -40,11 +40,6 @@ process UMITOOLS_GROUP {
$group_info \\
$paired \\
$args

cat <<-END_VERSIONS > versions.yml
"${task.process}":
umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
END_VERSIONS
"""

stub:
Expand All @@ -54,10 +49,5 @@ process UMITOOLS_GROUP {
touch ${prefix}.log
touch ${prefix}.tsv
$output_bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
umitools: \$( umi_tools --version | sed '/version:/!d; s/.*: //' )
END_VERSIONS
"""
}
36 changes: 25 additions & 11 deletions modules/nf-core/umitools/group/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -11,9 +11,9 @@ tools:
description: >
UMI-tools contains tools for dealing with Unique Molecular Identifiers (UMIs)/Random
Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes

documentation: https://umi-tools.readthedocs.io/en/latest/
license: ["MIT"]
license:
- "MIT"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -72,18 +72,32 @@ output:
e.g. [ id:'test', single_end:false ]
- "*.tsv":
type: file
description: Flatfile describing the read groups, see docs for complete info
of all columns
description: Flatfile describing the read groups, see docs for complete
info of all columns
pattern: "*.{tsv}"
ontologies:
- edam: http://edamontology.org/format_3475 # TSV
- edam: http://edamontology.org/format_3475
Comment thread
SPPearce marked this conversation as resolved.
versions_umitools:
- - ${task.process}:
type: string
description: The name of the process
- umitools:
type: string
description: The name of the tool
- "umi_tools --version | sed 's/UMI-tools version: //'":
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 name of the process
- umitools:
type: string
description: The name of the tool
- "umi_tools --version | sed 's/UMI-tools version: //'":
type: eval
description: The expression to obtain the version of the tool
authors:
- "@Joon-Klaps"
maintainers:
Expand Down
12 changes: 5 additions & 7 deletions modules/nf-core/umitools/group/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -86,10 +86,9 @@ nextflow_process {
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.tsv,
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
).match() }
sanitizeOutput(process.out, unstableKeys: ["log", "bam"])
).match() }
)
}

Expand All @@ -113,7 +112,7 @@ nextflow_process {
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
sanitizeOutput(process.out, unstableKeys: ["log", "bam"])
).match() }
)
}
Expand All @@ -136,10 +135,9 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out.tsv,
bam(process.out.bam[0][1]).getReadsMD5(),
file(process.out.log[0][1]).readLines()[0..1],
process.out.versions
sanitizeOutput(process.out, unstableKeys: ["log", "bam"])
).match() }
)
}
Expand All @@ -161,7 +159,7 @@ nextflow_process {
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}

Expand Down
173 changes: 110 additions & 63 deletions modules/nf-core/umitools/group/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -6,49 +6,46 @@
"# UMI-tools version: 1.1.6",
"# output generated by group -I test.bam --output-bam -S test_grouped.bam -L test_grouped.log --paired --random-seed=100"
],
[
"versions.yml:md5,f0c472387195b669228e3b390f8a93bf"
]
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-11T09:44:43.467038"
},
"with_umi - stub": {
"content": [
{
"0": [
"bam": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.log:md5,d41d8cd98f00b204e9800998ecf8427e"
"test_grouped.bam"
]
],
"1": [
"log": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
"test_grouped.log"
]
],
"2": [
"tsv": [

],
"versions_umitools": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
"UMITOOLS_GROUP",
"umitools",
"1.1.6"
]
],
"3": [
"versions.yml:md5,f0c472387195b669228e3b390f8a93bf"
],
]
}
],
"timestamp": "2026-06-18T06:15:31.228922956",
"meta": {
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"with_umi - stub": {
"content": [
{
"bam": [
[
{
Expand Down Expand Up @@ -76,66 +73,116 @@
"test_grouped.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,f0c472387195b669228e3b390f8a93bf"
"versions_umitools": [
[
"UMITOOLS_GROUP",
"umitools",
"1.1.6"
]
]
}
],
"timestamp": "2026-06-18T06:15:56.340264366",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-11T09:45:15.641582"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"no_umi": {
"content": [
"b01829d27fad55e707745f86311b443e",
[
[
{
"id": "test"
},
"test_grouped.tsv:md5,1a3ccdc00df59fa89c79ad482980a003"
]
],
[
"# UMI-tools version: 1.1.6",
"# output generated by group -I test.paired_end.sorted.bam --output-bam -S test_grouped.bam -L test_grouped.log --group-out test_grouped.tsv --paired --random-seed=100"
],
[
"versions.yml:md5,f0c472387195b669228e3b390f8a93bf"
]
{
"bam": [
[
{
"id": "test"
},
"test_grouped.bam"
]
],
"log": [
[
{
"id": "test"
},
"test_grouped.log"
]
],
"tsv": [
[
{
"id": "test"
},
"test_grouped.tsv:md5,1a3ccdc00df59fa89c79ad482980a003"
]
],
"versions_umitools": [
[
"UMITOOLS_GROUP",
"umitools",
"1.1.6"
]
]
}
],
"timestamp": "2026-06-18T06:15:17.067893237",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-11T09:44:24.962708"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
},
"with_umi - create bam and tsv": {
"content": [
[
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d652eb6570057e9e709e8cac5f43d00c"
]
],
"72da540b9a840cf39e3567cc35045143",
[
"# UMI-tools version: 1.1.6",
"# output generated by group -I test.bam --output-bam -S test_grouped.bam -L test_grouped.log --group-out test_grouped.tsv --paired --random-seed=100"
],
[
"versions.yml:md5,f0c472387195b669228e3b390f8a93bf"
]
{
"bam": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.bam"
]
],
"log": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.log"
]
],
"tsv": [
[
{
"id": "test",
"single_end": false
},
"test_grouped.tsv:md5,d652eb6570057e9e709e8cac5f43d00c"
]
],
"versions_umitools": [
[
"UMITOOLS_GROUP",
"umitools",
"1.1.6"
]
]
}
],
"timestamp": "2026-06-18T07:17:11.659317297",
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
},
"timestamp": "2025-09-11T09:45:01.696782"
"nf-test": "0.9.5",
"nextflow": "26.04.0"
}
}
}
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