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Merged
SPPearce merged 2 commits into from
Aug 3, 2026
Merged

Update to topic nanomonsv #12500

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a79bd1f
Update to topic
LouisLeNezet Aug 3, 2026
d3d766a
Fix conda env
LouisLeNezet Aug 3, 2026
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1 change: 1 addition & 0 deletions modules/nf-core/nanomonsv/parse/environment.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -4,5 +4,6 @@ channels:
- conda-forge
- bioconda
dependencies:
- bioconda::htslib=1.21
- bioconda::nanomonsv=0.8.0
- conda-forge::python=3.12.9
42 changes: 16 additions & 26 deletions modules/nf-core/nanomonsv/parse/main.nf
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Expand Up @@ -19,48 +19,38 @@ process NANOMONSV_PARSE {
tuple val(meta), path("${prefix}.rearrangement.sorted.bedpe.gz.tbi"), emit: rearrangements_index
tuple val(meta), path("${prefix}.bp_info.sorted.bed.gz") , emit: bp_info
tuple val(meta), path("${prefix}.bp_info.sorted.bed.gz.tbi") , emit: bp_info_index
path "versions.yml" , emit: versions
tuple val("${task.process}"), val('nanomonsv'), eval("nanomonsv --version 2>&1 | sed 's/^nanomonsv //'") , topic: versions, emit: versions_nanomonsv
tuple val("${task.process}"), val('mafft'), eval("mafft --version 2>&1 | sed 's/^v//; s/ (.*//'") , topic: versions, emit: versions_mafft
tuple val("${task.process}"), val('racon'), eval("racon --version 2>&1 | sed 's/^v//'") , topic: versions, emit: versions_racon
tuple val("${task.process}"), val('tabix'), eval("tabix --version 2>&1 | sed '1!d;s/^tabix (htslib) //'"), topic: versions, emit: versions_tabix
tuple val("${task.process}"), val('bgzip'), eval("bgzip --version 2>&1 | sed '1!d;s/^bgzip (htslib) //'"), topic: versions, emit: versions_bgzip
tuple val("${task.process}"), val('python'), eval("python3 --version | sed 's/Python //g'") , topic: versions, emit: versions_python

when:
task.ext.when == null || task.ext.when

script:
prefix = task.ext.prefix ?: "${meta.id}"
def args = task.ext.args ?: ''
"""
nanomonsv parse ${args} ${bam} ${prefix}

cat <<-END_VERSIONS > versions.yml
"${task.process}":
nanomonsv: \$(echo \$(nanomonsv --version 2>&1) | sed 's/^nanomonsv //')
mafft: \$(echo \$(mafft --version 2>&1) | sed 's/^v//; s/ (.*//')
racon: \$(echo \$(racon --version 2>&1) | sed 's/^v//')
tabix: \$(echo \$(tabix --version 2>&1) | sed 's/^tabix (htslib) //; s/ Copyright.*//')
bgzip: \$(echo \$(bgzip --version 2>&1) | sed 's/^bgzip (htslib) //; s/ Copyright.*//')
python: \$(python3 --version | sed 's/Python //g')
END_VERSIONS
"""
nanomonsv parse \\
${args} \\
${bam} \\
${prefix}
"""

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

"""
echo | gzip > ${prefix}.insertion.sorted.bed.gz
echo "" | gzip > ${prefix}.insertion.sorted.bed.gz
touch ${prefix}.insertion.sorted.bed.gz.tbi
echo | gzip > ${prefix}.deletion.sorted.bed.gz
echo "" | gzip > ${prefix}.deletion.sorted.bed.gz
touch ${prefix}.deletion.sorted.bed.gz.tbi
echo | gzip > ${prefix}.rearrangement.sorted.bedpe.gz
echo "" | gzip > ${prefix}.rearrangement.sorted.bedpe.gz
touch ${prefix}.rearrangement.sorted.bedpe.gz.tbi
echo | gzip > ${prefix}.bp_info.sorted.bed.gz
echo "" | gzip > ${prefix}.bp_info.sorted.bed.gz
touch ${prefix}.bp_info.sorted.bed.gz.tbi

cat <<-END_VERSIONS > versions.yml
"${task.process}":
nanomonsv: \$(echo \$(nanomonsv --version 2>&1) | sed 's/^nanomonsv //')
mafft: \$(echo \$(mafft --version 2>&1) | sed 's/^v//; s/ (.*//')
racon: \$(echo \$(racon --version 2>&1) | sed 's/^v//')
tabix: \$(echo \$(tabix --version 2>&1) | sed 's/^tabix (htslib) //; s/ Copyright.*//')
bgzip: \$(echo \$(bgzip --version 2>&1) | sed 's/^bgzip (htslib) //; s/ Copyright.*//')
python: \$(python3 --version | sed 's/Python //g')
END_VERSIONS
"""
}
145 changes: 135 additions & 10 deletions modules/nf-core/nanomonsv/parse/meta.yml
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Expand Up @@ -20,7 +20,8 @@ tools:
documentation: https://github.com/friend1ws/nanomonsv#commands
tool_dev_url: https://github.com/friend1ws/nanomonsv
doi: "10.1101/2020.07.22.214262 "
licence: ["GPL v3"]
licence:
- "GPL v3"
identifier: ""
input:
- - meta:
Expand Down Expand Up @@ -58,7 +59,8 @@ output:
e.g. [ id:'test', single_end:false ]
- ${prefix}.insertion.sorted.bed.gz.tbi:
type: file
description: Index for gzipped BED file containing reads supporting insertions
description: Index for gzipped BED file containing reads supporting
insertions
pattern: "*.{bed.gz.tbi}"
ontologies: []
deletions:
Expand All @@ -80,7 +82,8 @@ output:
e.g. [ id:'test', single_end:false ]
- ${prefix}.deletion.sorted.bed.gz.tbi:
type: file
description: Index for gzipped BED file containing reads supporting deletions
description: Index for gzipped BED file containing reads supporting
deletions
pattern: "*.{bed.gz.tbi}"
ontologies: []
rearrangements:
Expand All @@ -102,7 +105,8 @@ output:
e.g. [ id:'test', single_end:false ]
- ${prefix}.rearrangement.sorted.bedpe.gz.tbi:
type: file
description: Index for gzipped BED file containing reads supporting rearrangements
description: Index for gzipped BED file containing reads supporting
rearrangements
pattern: "*.{bed.gz.tbi}"
ontologies: []
bp_info:
Expand All @@ -127,13 +131,134 @@ output:
description: Index for gzipped BED file containing breakpoint info
pattern: "*.{bed.gz.tbi}"
ontologies: []
versions_nanomonsv:
- - ${task.process}:
type: string
description: The name of the process
- nanomonsv:
type: string
description: The name of the tool
- nanomonsv --version 2>&1 | sed 's/^nanomonsv //':
type: eval
description: The expression to obtain the version of the tool

versions_mafft:
- - ${task.process}:
type: string
description: The name of the process
- mafft:
type: string
description: The name of the tool
- mafft --version 2>&1 | sed 's/^v//; s/ (.*//':
type: eval
description: The expression to obtain the version of the tool

versions_racon:
- - ${task.process}:
type: string
description: The name of the process
- racon:
type: string
description: The name of the tool
- racon --version 2>&1 | sed 's/^v//':
type: eval
description: The expression to obtain the version of the tool

versions_tabix:
- - ${task.process}:
type: string
description: The name of the process
- tabix:
type: string
description: The name of the tool
- tabix --version 2>&1 | sed '1!d;s/^tabix (htslib) //':
type: eval
description: The expression to obtain the version of the tool

versions_bgzip:
- - ${task.process}:
type: string
description: The name of the process
- bgzip:
type: string
description: The name of the tool
- bgzip --version 2>&1 | sed '1!d;s/^bgzip (htslib) //':
type: eval
description: The expression to obtain the version of the tool

versions_python:
- - ${task.process}:
type: string
description: The name of the process
- python:
type: string
description: The name of the tool
- python3 --version | sed 's/Python //g':
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
- nanomonsv:
type: string
description: The name of the tool
- nanomonsv --version 2>&1 | sed 's/^nanomonsv //':
type: eval
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The name of the process
- mafft:
type: string
description: The name of the tool
- mafft --version 2>&1 | sed 's/^v//; s/ (.*//':
type: eval
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The name of the process
- racon:
type: string
description: The name of the tool
- racon --version 2>&1 | 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
- tabix:
type: string
description: The name of the tool
- tabix --version 2>&1 | sed '1!d;s/^tabix (htslib) //':
type: eval
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The name of the process
- bgzip:
type: string
description: The name of the tool
- bgzip --version 2>&1 | sed '1!d;s/^bgzip (htslib) //':
type: eval
description: The expression to obtain the version of the tool

- - ${task.process}:
type: string
description: The name of the process
- python:
type: string
description: The name of the tool
- python3 --version | sed 's/Python //g':
type: eval
description: The expression to obtain the version of the tool

authors:
- "@awgymer"
maintainers:
Expand Down
31 changes: 12 additions & 19 deletions modules/nf-core/nanomonsv/parse/tests/main.nf.test
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Expand Up @@ -14,20 +14,18 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of(
[
[id:'control'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists:true)
]
)
input[0] = [
[id:'control'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand All @@ -37,23 +35,18 @@ nextflow_process {
when {
process {
"""
input[0] = Channel.of(
[
[id:'control'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists:true)
]
)
input[0] = [
[id:'control'],
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam', checkIfExists:true),
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/nanopore/bam/test.sorted.bam.bai', checkIfExists:true)
]
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(
process.out,
path(process.out.versions[0]).yaml
).match() }
{ assert snapshot(sanitizeOutput(process.out)).match() }
)
}
}
Expand Down
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