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Merged
SPPearce merged 4 commits into from
Jan 7, 2026
Merged

Swap mosdepth to topic #9612

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660090c
Swap mosdepth to topic
SPPearce Dec 31, 2025
754e457
Fail the test that should fail
SPPearce Dec 31, 2025
ea2c2ef
Prettier
SPPearce Jan 5, 2026
922c95c
Update args check
SPPearce Jan 7, 2026
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3 changes: 1 addition & 2 deletions modules/nf-core/mosdepth/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -5,6 +5,5 @@ channels:
- bioconda
dependencies:
# renovate: datasource=conda depName=bioconda/mosdepth
- mosdepth=0.3.11=h0ec343a_1
# renovate: datasource=conda depName=bioconda/htslib
- htslib=1.22.1
- mosdepth=0.3.11=h0ec343a_1
19 changes: 8 additions & 11 deletions modules/nf-core/mosdepth/main.nf
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Expand Up @@ -24,7 +24,7 @@ process MOSDEPTH {
tuple val(meta), path('*.quantized.bed.gz.csi') , optional:true, emit: quantized_csi
tuple val(meta), path('*.thresholds.bed.gz') , optional:true, emit: thresholds_bed
tuple val(meta), path('*.thresholds.bed.gz.csi'), optional:true, emit: thresholds_csi
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('mosdepth'), eval("mosdepth --version | sed 's/mosdepth //g'"), topic: versions, emit: versions_mosdepth

when:
task.ext.when == null || task.ext.when
Expand All @@ -49,15 +49,17 @@ process MOSDEPTH {
$args \\
$prefix \\
$bam

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

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.id}"
if (bed && args.contains("--by")) {
error "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
}
if (!bed && args.contains("--thresholds")) {
error "'--thresholds' can only be specified in conjunction with '--by'"
}
"""
touch ${prefix}.global.dist.txt
touch ${prefix}.region.dist.txt
Expand All @@ -71,10 +73,5 @@ process MOSDEPTH {
touch ${prefix}.quantized.bed.gz.csi
echo "" | gzip > ${prefix}.thresholds.bed.gz
touch ${prefix}.thresholds.bed.gz.csi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
END_VERSIONS
"""
}
28 changes: 21 additions & 7 deletions modules/nf-core/mosdepth/meta.yml
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Expand Up @@ -178,20 +178,34 @@ output:
description: Index file for BED file with threshold coverage
pattern: "*.{thresholds.bed.gz.csi}"
ontologies: []
versions_mosdepth:
- - ${task.process}:
type: string
description: The process the versions were collected from
- mosdepth:
type: string
description: The tool name
- "mosdepth --version | sed 's/mosdepth //g'":
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
- mosdepth:
type: string
description: The tool name
- "mosdepth --version | sed 's/mosdepth //g'":
type: string
description: The command used to generate the version of the tool
authors:
- "@joseespinosa"
- "@drpatelh"
- "@ramprasadn"
- "@matthdsm"
maintainers:
- "@joseespinosa"
- "@drpatelh"
- "@ramprasadn"
- "@matthdsm"
68 changes: 45 additions & 23 deletions modules/nf-core/mosdepth/tests/main.nf.test
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Expand Up @@ -7,10 +7,14 @@ nextflow_process {
tag "modules"
tag "modules_nfcore"
tag "mosdepth"
config "./nextflow.config"

test("homo_sapiens - bam, bai, []") {

when {
params {
module_args = ""
}
process {
"""
input[0] = [
Expand All @@ -25,9 +29,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

Expand All @@ -36,6 +40,9 @@ nextflow_process {
test("homo_sapiens - bam, bai, bed") {

when {
params {
module_args = ""
}
process {
"""
input[0] = [
Expand All @@ -50,9 +57,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

Expand All @@ -61,6 +68,9 @@ nextflow_process {
test("homo_sapiens - cram, crai, []") {

when {
params {
module_args = ""
}
process {
"""
input[0] = [
Expand All @@ -78,9 +88,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

Expand All @@ -89,6 +99,9 @@ nextflow_process {
test("homo_sapiens - cram, crai, bed") {

when {
params {
module_args = ""
}
process {
"""
input[0] = [
Expand All @@ -106,18 +119,20 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

}

test("homo_sapiens - bam, bai, [] - window") {

config "./window.config"
when {
params {
module_args = "--by 100"
}
process {
"""
input[0] = [
Expand All @@ -132,18 +147,20 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

}

test("homo_sapiens - bam, bai, [] - quantized") {

config "./quantized.config"
when {
params {
module_args = "--quantize 0:1:4:100:200"
}
process {
"""
input[0] = [
Expand All @@ -158,18 +175,20 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

}

test("homo_sapiens - bam, bai, bed - thresholds") {

config "./threshold.config"
when {
params {
module_args = "--thresholds 1,10,20,30"
}
process {
"""
input[0] = [
Expand All @@ -184,18 +203,20 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

}

test("homo_sapiens - bam, bai, bed - fail") {

config "./window.config"
when {
params {
module_args = "--by 100"
}
process {
"""
input[0] = [
Expand All @@ -210,9 +231,7 @@ nextflow_process {
}

then {
assertAll(
{ assert process.failed }
)
assert process.failed
}

}
Expand All @@ -221,6 +240,9 @@ nextflow_process {

options "-stub"
when {
params {
module_args = ""
}
process {
"""
input[0] = [
Expand All @@ -235,9 +257,9 @@ nextflow_process {
}

then {
assert process.success
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(process.out).match()}
)
}

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