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Add module openms/idmassaccuracy (#6647)
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* Setup cometadapter module

* cometadapter draft

* finalize tests

* remove defaults

* enclosing input as channel

* replace collect with map

* add channel of again

* fix input channles by joining them

* update correct snapshot

* fix lint

* fix snapshots, comet writes timestamps in output file

* prettier

* Update environment.yml

* strip out suffix version tag, which differs between container and conda

* move to version content check instead of hash

* align conda version and container version tag

* add idmassaccuracy module

* shorten version parsing

---------

Co-authored-by: Simon Pearce <[email protected]>
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@jonasscheid @SPPearce
jonasscheid and SPPearce authored Sep 16, 2024
1 parent e2b2fde commit f768b28
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5 changes: 5 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/environment.yml
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channels:
- conda-forge
- bioconda
dependencies:
- "bioconda::openms=3.1.0"
52 changes: 52 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/main.nf
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process OPENMS_IDMASSACCURACY {
tag "$meta.id"
label 'process_single'

conda "${moduleDir}/environment.yml"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms:3.1.0--h191ead1_4' :
'biocontainers/openms:3.1.0--h191ead1_4' }"

input:
tuple val(meta), path(mzmls), path(idxmls)

output:
tuple val(meta), path("*frag_mass_err.tsv") , emit: frag_err
tuple val(meta), path("*prec_mass_err.tsv") , emit: prec_err, optional: true
path "versions.yml" , emit: versions

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

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

"""
IDMassAccuracy \\
-in $mzmls \\
-id_in $idxmls \\
-out_fragment ${prefix}_frag_mass_err.tsv \\
-threads $task.cpus \\
$args
cat <<-END_VERSIONS > versions.yml
"${task.process}":
OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1)
END_VERSIONS
"""

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

"""
touch ${prefix}_frag_mass_err.tsv
touch ${prefix}_prec_mass_err.tsv
cat <<-END_VERSIONS > versions.yml
"${task.process}":
OpenMS: \$(FileInfo 2>&1 | grep -E '^Version(.*)' | cut -d ' ' -f 2 | cut -d '-' -f 1)
END_VERSIONS
"""
}
55 changes: 55 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/meta.yml
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name: "openms_idmassaccuracy"
description: Calculates a distribution of the mass error from given mass spectra and IDs.
keywords:
- mass_error
- openms
- proteomics
tools:
- "openms":
description: "OpenMS is an open-source software C++ library for LC-MS data management and analyses"
homepage: "https://openms.de"
documentation: "https://openms.readthedocs.io/en/latest/index.html"
tool_dev_url: "https://github.com/OpenMS/OpenMS"
doi: "10.1038/s41592-024-02197-7"
licence: ["BSD"]

input:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'test' ]`
- mzmls:
type: file
description: |
List containing one or more mzML files
e.g. `[ 'file1.mzML', 'file2.mzML' ]`
pattern: "*.{mzML}"
- idxmls:
type: file
description: |
List containing one or more idXML files
e.g. `[ 'file1.idXML', 'file2.idXML' ]`
pattern: "*.{idXML}"

output:
- meta:
type: map
description: |
Groovy Map containing sample information
e.g. `[ id:'test' ]`
- versions:
type: file
description: File containing software versions
pattern: "versions.yml"
- frag_err:
type: file
description: TSV file containing the fragment mass errors
pattern: "*frag_mass_err.{tsv}"
- prec_err:
type: file
description: Optional TSV file containing the precursor mass errors
pattern: "*prec_mass_err.{tsv}"

authors:
- "@jonasscheid"
81 changes: 81 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/tests/main.nf.test
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nextflow_process {

name "Test Process OPENMS_IDMASSACCURACY"
script "../main.nf"
process "OPENMS_IDMASSACCURACY"
config "./nextflow.config"

tag "modules"
tag "modules_nfcore"
tag "openms"
tag "openms/idmassaccuracy"
tag "thermorawfileparser"
tag "openms/decoydatabase"
tag "openmsthirdparty/cometadapter"

setup {
run("THERMORAWFILEPARSER") {
script "../../../thermorawfileparser/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test'],
file(params.modules_testdata_base_path + 'proteomics/msspectra/PXD012083_e005640_II.raw', checkIfExists: true)
])
"""
}
}
run("OPENMS_DECOYDATABASE") {
script "../../../openms/decoydatabase/main.nf"
process {
"""
input[0] = Channel.of([
[ id:'test'],
file(params.modules_testdata_base_path + 'proteomics/database/UP000005640_9606.fasta', checkIfExists: true)
])
"""
}
}
run("OPENMSTHIRDPARTY_COMETADAPTER") {
script "../../../openmsthirdparty/cometadapter/main.nf"
process {
"""
input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMS_DECOYDATABASE.out.decoy_fasta)
"""
}
}
}

test("proteomics - openms - mass_error") {
when {
process {
"""
input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("proteomics - openms - mass_error - stub") {
options "-stub"
when {
process {
"""
input[0] = THERMORAWFILEPARSER.out.spectra.join(OPENMSTHIRDPARTY_COMETADAPTER.out.idxml)
"""
}
}
then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}
}
90 changes: 90 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/tests/main.nf.test.snap
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{
"proteomics - openms - mass_error - stub": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_frag_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"1": [
[
{
"id": "test"
},
"test_prec_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"2": [
"versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
],
"frag_err": [
[
{
"id": "test"
},
"test_frag_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"prec_err": [
[
{
"id": "test"
},
"test_prec_mass_err.tsv:md5,d41d8cd98f00b204e9800998ecf8427e"
]
],
"versions": [
"versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-16T05:12:06.655389198"
},
"proteomics - openms - mass_error": {
"content": [
{
"0": [
[
{
"id": "test"
},
"test_frag_mass_err.tsv:md5,c659254bc1305edde65eca890a6cf36f"
]
],
"1": [

],
"2": [
"versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
],
"frag_err": [
[
{
"id": "test"
},
"test_frag_mass_err.tsv:md5,c659254bc1305edde65eca890a6cf36f"
]
],
"prec_err": [

],
"versions": [
"versions.yml:md5,84212cbbf016bbcae0eb1bb0fcc30db7"
]
}
],
"meta": {
"nf-test": "0.9.0",
"nextflow": "24.04.4"
},
"timestamp": "2024-09-16T05:11:55.087464408"
}
}
27 changes: 27 additions & 0 deletions modules/nf-core/openms/idmassaccuracy/tests/nextflow.config
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process {

withName:OPENMSTHIRDPARTY_COMETADAPTER {
ext.args = [
"-instrument low_res",
"-fragment_bin_offset 0.4",
"-precursor_mass_tolerance 5",
"-precursor_error_units 'ppm'",
"-fragment_mass_tolerance 0.50025",
"-digest_mass_range '800:5000'",
"-max_variable_mods_in_peptide 1",
"-precursor_charge '2:5'",
"-activation_method 'CID'",
"-variable_modifications 'Oxidation (M)'",
"-enzyme 'unspecific cleavage'",
"-spectrum_batch_size 0"
].join(' ').trim()
}

withName:OPENMS_IDMASSACCURACY {
ext.args = [
"-precursor_error_ppm",
"-fragment_mass_tolerance 0.50025"
].join(' ').trim()
}

}

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