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Merged
ypriverol merged 7 commits into from
Mar 7, 2025
Merged

quantms-rescoring changed 0.0.5 #489

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71782f3
quantms-rescoring changed 0.0.5
ypriverol Mar 5, 2025
71aa330
quantms-rescoring changed 0.0.5
ypriverol Mar 6, 2025
01b6eb0
Updating error in openms 3.3.0 version docker
ypriverol Mar 6, 2025
c3d226e
Merge pull request #54 from ypriverol/dev
daichengxin Mar 6, 2025
5709c1e
update ms2rescore
daichengxin Mar 7, 2025
1561663
Update main.nf
daichengxin Mar 7, 2025
b48b9da
Merge pull request #5 from daichengxin/dev
ypriverol Mar 7, 2025
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2 changes: 0 additions & 2 deletions conf/modules.config
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Expand Up @@ -258,9 +258,7 @@ process {
withName: 'MS2RESCORE' {
ext.args = [
"--ms2pip_model ${params.ms2pip_model}",
"--rescoring_engine 'percolator'",
"--calibration_set_size ${params.calibration_set_size}",
"--test_fdr ${params.test_FDR}",
params.feature_generators.trim() ? "--feature_generators ${params.feature_generators}" : ''
].join(' ').trim()
publishDir = [
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30 changes: 0 additions & 30 deletions modules/local/add_sage_feat/main.nf
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39 changes: 0 additions & 39 deletions modules/local/add_sage_feat/meta.yml
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37 changes: 13 additions & 24 deletions modules/local/ms2rescore/main.nf
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Expand Up @@ -2,10 +2,10 @@ process MS2RESCORE {
tag "$meta.mzml_id"
label 'process_high'

conda "bioconda::quantms-rescoring=0.0.4"
conda "bioconda::quantms-rescoring=0.0.5"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.4--pyhdfd78af_0' :
'biocontainers/quantms-rescoring:0.0.4--pyhdfd78af_0' }"
'https://depot.galaxyproject.org/singularity/quantms-rescoring:0.0.5--pyhdfd78af_0' :
'biocontainers/quantms-rescoring:0.0.5--pyhdfd78af_0' }"

// userEmulation settings when docker is specified
containerOptions = (workflow.containerEngine == 'docker') ? '-u $(id -u) -e "HOME=${HOME}" -v /etc/passwd:/etc/passwd:ro -v /etc/shadow:/etc/shadow:ro -v /etc/group:/etc/group:ro -v $HOME:$HOME' : ''
Expand All @@ -15,7 +15,6 @@ process MS2RESCORE {

output:
tuple val(meta), path("*ms2rescore.idXML") , emit: idxml
tuple val(meta), path("*feature_names.tsv"), emit: feature_names
tuple val(meta), path("*.html" ) , optional:true, emit: html
path "versions.yml" , emit: versions
path "*.log" , emit: log
Expand All @@ -32,8 +31,8 @@ process MS2RESCORE {
if (meta['fragmentmasstoleranceunit'].toLowerCase().endsWith('da')) {
ms2_tolerence = meta['fragmentmasstolerance']
} else {
log.info "Warning: MS2Rescore only supports Da unit. Set default ms2 tolerance as 0.02!"
ms2_tolerence = 0.02
log.info "Warning: MS2Rescore only supports Da unit. Set default ms2 tolerance as 0.05!"
ms2_tolerence = 0.05
}

if (params.decoy_string_position == "prefix") {
Expand All @@ -43,11 +42,11 @@ process MS2RESCORE {
}

"""
rescoring ms2rescore \\
--psm_file $idxml \\
--spectrum_path $mzml \\
rescoring msrescore2feature \\
--idxml $idxml \\
--mzml $mzml \\
--ms2_tolerance $ms2_tolerence \\
--output_path ${idxml.baseName}_ms2rescore.idXML \\
--output ${idxml.baseName}_ms2rescore.idXML \\
--ms2pip_model_dir ${params.ms2pip_model_dir} \\
--processes $task.cpus \\
--id_decoy_pattern $decoy_pattern \\
Expand All @@ -56,20 +55,10 @@ process MS2RESCORE {

cat <<-END_VERSIONS > versions.yml
"${task.process}":
MS2Rescore: \$(echo \$(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \\(v\\K[^\\)]+' )
END_VERSIONS
"""

stub:
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.mzml_id}_ms2rescore"

"""
touch ${prefix}.idXML

cat <<-END_VERSIONS > versions.yml
"${task.process}":
MS2Rescore: \$(echo \$(ms2rescore --version 2>&1) | grep -oP 'MS²Rescore \\(v\\K[^\\)]+' )
quantms-rescoring: \$(echo \$(rescoring --version 2>&1) | sed 's/quantmsrescore: //g' | cut -d ' ' -f 2)
ms2pip: \$(echo \$(ms2pip --version 2>&1) | grep version | sed 's/version: //g' | cut -d ' ' -f 3)
deeplc: \$(echo \$(deeplc --version 2>&1))
MS2Rescore: \$(echo \$(ms2rescore --version 2>&1) | awk '{print \$NF}')
END_VERSIONS
"""
}
4 changes: 0 additions & 4 deletions modules/local/ms2rescore/meta.yml
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Expand Up @@ -26,10 +26,6 @@ output:
type: file
description: idXML identification file after MS2 rescoring
pattern: "*.idXML"
- feature_names:
type: file
description: File containing feature names
pattern: "*feature_names.tsv"
- version:
type: file
description: File containing software version
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4 changes: 2 additions & 2 deletions modules/local/openms/consensusid/main.nf
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Expand Up @@ -5,8 +5,8 @@ process CONSENSUSID {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), val(qval_score)
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4 changes: 2 additions & 2 deletions modules/local/openms/decoydatabase/main.nf
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Expand Up @@ -4,8 +4,8 @@ process DECOYDATABASE {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
path(db_for_decoy)
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4 changes: 2 additions & 2 deletions modules/local/openms/epifany/main.nf
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Expand Up @@ -4,8 +4,8 @@ process EPIFANY {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(consus_file)
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12 changes: 3 additions & 9 deletions modules/local/openms/extractpsmfeatures/main.nf
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Expand Up @@ -6,11 +6,11 @@ process EXTRACTPSMFEATURES {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), path(extra_feat)
tuple val(meta), path(id_file)

output:
tuple val(meta), path("${id_file.baseName}_feat.idXML"), emit: id_files_feat
Expand All @@ -21,17 +21,11 @@ process EXTRACTPSMFEATURES {
def args = task.ext.args ?: ''
def prefix = task.ext.prefix ?: "${meta.mzml_id}"

feature = ""
if (params.ms2rescore) {
feature = "-extra \$(awk 'NR > 1 && \$1 !~ /psm_file/ {printf \"%s \", \$2}' ${extra_feat})"
}

"""
PSMFeatureExtractor \\
-in ${id_file} \\
-out ${id_file.baseName}_feat.idXML \\
-threads $task.cpus \\
${feature} \\
$args \\
2>&1 | tee ${id_file.baseName}_extract_psm_feature.log

Expand Down
4 changes: 2 additions & 2 deletions modules/local/openms/falsediscoveryrate/main.nf
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Expand Up @@ -6,8 +6,8 @@ process FALSEDISCOVERYRATE {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/filemerge/main.nf
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Expand Up @@ -5,8 +5,8 @@ process FILEMERGE {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
file(id_map)
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4 changes: 2 additions & 2 deletions modules/local/openms/idconflictresolver/main.nf
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Expand Up @@ -4,8 +4,8 @@ process IDCONFLICTRESOLVER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
path consus_file
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4 changes: 2 additions & 2 deletions modules/local/openms/idfilter/main.nf
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Expand Up @@ -6,8 +6,8 @@ process IDFILTER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/idmapper/main.nf
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Expand Up @@ -5,8 +5,8 @@ process IDMAPPER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), path(map_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/idmerger/main.nf
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Expand Up @@ -5,8 +5,8 @@ process IDMERGER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_files), val(groupkey)
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4 changes: 2 additions & 2 deletions modules/local/openms/idripper/main.nf
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Expand Up @@ -5,8 +5,8 @@ process IDRIPPER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), val(qval_score)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/openms/idscoreswitcher/main.nf
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Expand Up @@ -6,8 +6,8 @@ process IDSCORESWITCHER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), val(new_score)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/openms/indexpeptides/main.nf
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Expand Up @@ -5,8 +5,8 @@ process INDEXPEPTIDES {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(id_file), path(database)
Expand Down
4 changes: 2 additions & 2 deletions modules/local/openms/isobaricanalyzer/main.nf
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Expand Up @@ -5,8 +5,8 @@ process ISOBARICANALYZER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(mzml_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/msstatsconverter/main.nf
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Expand Up @@ -5,8 +5,8 @@ process MSSTATSCONVERTER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
path consensusXML
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4 changes: 2 additions & 2 deletions modules/local/openms/mzmlindexing/main.nf
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Expand Up @@ -5,8 +5,8 @@ process MZMLINDEXING {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(mzmlfile)
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4 changes: 2 additions & 2 deletions modules/local/openms/openmspeakpicker/main.nf
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Expand Up @@ -5,8 +5,8 @@ process OPENMSPEAKPICKER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(mzml_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/proteininference/main.nf
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Expand Up @@ -4,8 +4,8 @@ process PROTEININFERENCE {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
tuple val(meta), path(consus_file)
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4 changes: 2 additions & 2 deletions modules/local/openms/proteinquantifier/main.nf
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Expand Up @@ -5,8 +5,8 @@ process PROTEINQUANTIFIER {

conda "bioconda::openms-thirdparty=3.3.0"
container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_4' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_4' }"
'https://depot.galaxyproject.org/singularity/openms-thirdparty:3.3.0--h9ee0642_8' :
'biocontainers/openms-thirdparty:3.3.0--h9ee0642_8' }"

input:
path epi_filt_resolve
Expand Down
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