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Update to topic pmdtools #12606

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LouisLeNezet Aug 6, 2026
666a73f
Update env
LouisLeNezet Aug 6, 2026
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1 change: 1 addition & 0 deletions modules/nf-core/pmdtools/filter/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,3 +6,4 @@ channels:
dependencies:
- bioconda::pmdtools=0.60
- bioconda::samtools=1.14
- conda-forge::python=3.9.7
31 changes: 10 additions & 21 deletions modules/nf-core/pmdtools/filter/main.nf
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Expand Up @@ -14,7 +14,8 @@ process PMDTOOLS_FILTER {

output:
tuple val(meta), path("*.bam"), emit: bam
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('pmdtools'), eval("pmdtools --version | sed 's/.*v//'") , topic: versions, emit: versions_pmdtools
tuple val("${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 @@ -25,45 +26,33 @@ process PMDTOOLS_FILTER {
def args3 = task.ext.args3 ?: ''
def split_cpus = Math.floor(task.cpus/2)
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${bam}" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
//threshold and header flags activate filtering function of pmdtools
"""
samtools \\
calmd \\
$bam \\
$reference \\
$args \\
${bam} \\
${reference} \\
${args} \\
-@ ${split_cpus} \\
| pmdtools \\
--threshold $threshold \\
--threshold ${threshold} \\
--header \\
$args2 \\
${args2} \\
| samtools \\
view \\
$args3 \\
${args3} \\
-Sb \\
- \\
-@ ${split_cpus} \\
-o ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pmdtools: \$( pmdtools --version | cut -f2 -d ' ' | sed 's/v//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""

stub:
def prefix = task.ext.prefix ?: "${meta.id}"
if ("$bam" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
if ("${bam}" == "${prefix}.bam") error "[pmdtools/filter] Input and output names are the same, use \"task.ext.prefix\" to disambiguate!"
//threshold and header flags activate filtering function of pmdtools
"""
touch ${prefix}.bam

cat <<-END_VERSIONS > versions.yml
"${task.process}":
pmdtools: \$( pmdtools --version | cut -f2 -d ' ' | sed 's/v//')
samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
END_VERSIONS
"""
}
52 changes: 45 additions & 7 deletions modules/nf-core/pmdtools/filter/meta.yml
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Expand Up @@ -12,7 +12,8 @@ tools:
documentation: https://github.com/pontussk/PMDtools
tool_dev_url: https://github.com/pontussk/PMDtools
doi: "10.1073/pnas.1318934111"
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -50,13 +51,50 @@ output:
description: Filtered BAM file
pattern: "*.bam"
ontologies: []
versions_pmdtools:
- - ${task.process}:
type: string
description: The name of the process
- pmdtools:
type: string
description: The name of the tool
- pmdtools --version | sed 's/.*v//':
type: eval
description: The expression to obtain the version of the tool

versions_samtools:
- - ${task.process}:
type: string
description: The name of the process
- samtools:
type: string
description: The name of the tool
- samtools version | sed '1!d;s/.* //':
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
- pmdtools:
type: string
description: The name of the tool
- pmdtools --version | sed 's/.*v//':
type: eval
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The name of the process
- samtools:
type: string
description: The name of the tool
- samtools version | sed '1!d;s/.* //':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@alexandregilardet"
maintainers:
Expand Down
32 changes: 14 additions & 18 deletions modules/nf-core/pmdtools/filter/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -16,13 +16,12 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = 3
input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]

input[1] = 3
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
"""
}
}
Expand All @@ -31,11 +30,9 @@ nextflow_process {
assertAll(
{ assert process.success },
{ assert snapshot(
bam(process.out.bam[0][1]).getReadsMD5(),
process.out.versions,
file(process.out.versions[0]).readLines()[1..2].collect { it.trim() } // Trap to catch conda version mismatches
).match()
}
bam(process.out.bam[0][1]).getReadsMD5(),
sanitizeOutput(process.out, unstableKeys:["bam"])
).match()}
)
}
}
Expand All @@ -47,21 +44,20 @@ nextflow_process {
process {
"""
input[0] = [
[ id:'test', single_end:false ], // meta map
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) ],
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true) ]
[ id:'test' ],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
]
input[1] = 3
input[2] = [ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ]

input[1] = 3
input[2] = file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
73 changes: 44 additions & 29 deletions modules/nf-core/pmdtools/filter/tests/main.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -2,53 +2,68 @@
"test-pmdtools-filter": {
"content": [
"665610db11378e0a02ab7d407a9d54c1",
[
"versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
],
[
"pmdtools: 0.50",
"samtools: 1.14"
]
{
"bam": [
[
{
"id": "test"
},
"test.bam"
]
],
"versions_pmdtools": [
[
"PMDTOOLS_FILTER",
"pmdtools",
"0.50"
]
],
"versions_samtools": [
[
"PMDTOOLS_FILTER",
"samtools",
"1.14"
]
]
}
],
"timestamp": "2026-08-06T15:52:16.062661885",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-29T12:54:08.428303"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
},
"test-pmdtools-filter-stub": {
"content": [
{
"0": [
"bam": [
[
{
"id": "test",
"single_end": false
"id": "test"
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
"versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
],
"bam": [
"versions_pmdtools": [
[
{
"id": "test",
"single_end": false
},
"test.bam:md5,d41d8cd98f00b204e9800998ecf8427e"
"PMDTOOLS_FILTER",
"pmdtools",
"0.50"
]
],
"versions": [
"versions.yml:md5,877c304e79e6d045661081ddd47bddd6"
"versions_samtools": [
[
"PMDTOOLS_FILTER",
"samtools",
"1.14"
]
]
}
],
"timestamp": "2026-08-06T15:52:22.821082671",
"meta": {
"nf-test": "0.8.4",
"nextflow": "24.04.4"
},
"timestamp": "2024-08-29T12:40:43.138953"
"nf-test": "0.9.5",
"nextflow": "26.04.6"
}
}
}