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Merged
SPPearce merged 4 commits into from
Dec 22, 2025
Merged

Swap mpileup to topics #9595

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ecd414b
Swap mpileup to topics
SPPearce Dec 21, 2025
72db77a
Apply suggestions from code review
SPPearce Dec 21, 2025
73b1aa6
Add Harshil back as author
SPPearce Dec 22, 2025
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SPPearce Dec 22, 2025
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12 changes: 1 addition & 11 deletions modules/nf-core/samtools/mpileup/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,7 @@ process SAMTOOLS_MPILEUP {

output:
tuple val(meta), path("*.mpileup.gz"), emit: mpileup
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 @@ -31,21 +31,11 @@ process SAMTOOLS_MPILEUP {
$intervals_cmd \\
$input
bgzip ${prefix}.mpileup

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}"
"""
echo | gzip > ${prefix}.mpileup.gz

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/mpileup/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -54,16 +54,31 @@ output:
description: mpileup file
pattern: "*.{mpileup}"
ontologies: []
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: 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: Name of the process
- samtools:
type: string
description: Name of the tool
- samtools --version | head -1 | sed -e "s/samtools //":
type: eval
description: The expression to obtain the version of the tool

authors:
- "@drpatelh"
- "@joseespinosa"
maintainers:
- "@drpatelh"
- "@joseespinosa"
15 changes: 3 additions & 12 deletions modules/nf-core/samtools/mpileup/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -27,10 +27,7 @@ nextflow_process {
then {
assert process.success
assertAll(
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match()}
)
}
}
Expand All @@ -56,10 +53,7 @@ nextflow_process {
then {
assert process.success
assertAll(
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match()}
)
}
}
Expand All @@ -82,10 +76,7 @@ nextflow_process {
then {
assert process.success
assertAll(
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(process.out).match()}
)
}
}
Expand Down
75 changes: 42 additions & 33 deletions modules/nf-core/samtools/mpileup/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,11 @@
]
],
"1": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
],
"mpileup": [
[
Expand All @@ -21,21 +25,20 @@
"test.mpileup.gz:md5,72340047c1feda82fa632d1762080bd8"
]
],
"versions": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
"versions_samtools": [
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
]
},
{
"SAMTOOLS_MPILEUP": {
"samtools": "1.22.1"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:39:24.687853"
"timestamp": "2025-12-22T08:56:18.583305677"
},
"bam_bed --stub": {
"content": [
Expand All @@ -49,7 +52,11 @@
]
],
"1": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
],
"mpileup": [
[
Expand All @@ -59,21 +66,20 @@
"test.mpileup.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
]
],
"versions": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
"versions_samtools": [
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
]
},
{
"SAMTOOLS_MPILEUP": {
"samtools": "1.22.1"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:39:35.387828"
"timestamp": "2025-12-22T08:54:55.388446375"
},
"bam_bed_fasta": {
"content": [
Expand All @@ -87,7 +93,11 @@
]
],
"1": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
],
"mpileup": [
[
Expand All @@ -97,20 +107,19 @@
"test.mpileup.gz:md5,958e6bead4103d72026f80153b6b5150"
]
],
"versions": [
"versions.yml:md5,e5a70b6d7e2c2ff0c2c63b66b7adb281"
"versions_samtools": [
[
"SAMTOOLS_MPILEUP",
"samtools",
"1.22.1"
]
]
},
{
"SAMTOOLS_MPILEUP": {
"samtools": "1.22.1"
}
}
],
"meta": {
"nf-test": "0.9.2",
"nextflow": "25.04.6"
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2025-09-10T14:39:29.744452"
"timestamp": "2025-12-22T08:56:25.883836102"
}
}
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