mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 11:38:17 +00:00
33 lines
1 KiB
Text
33 lines
1 KiB
Text
|
process MAXQUANT_LFQ {
|
||
|
|
tag "$meta.id"
|
||
|
|
label 'process_long'
|
||
|
|
|
||
|
|
conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
|
||
|
|
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||
|
|
container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
|
||
|
|
} else {
|
||
|
|
container "wombatp/maxquant-pipeline:v0.13"
|
||
|
|
}
|
||
|
|
|
||
|
|
input:
|
||
|
|
tuple val(meta), path(fasta), path(paramfile)
|
||
|
|
path raw
|
||
|
|
|
||
|
|
output:
|
||
|
|
tuple val(meta), path("*.txt"), emit: maxquant_txt
|
||
|
|
path "versions.yml" , emit: version
|
||
|
|
|
||
|
|
script:
|
||
|
|
def args = task.ext.args ?: ''
|
||
|
|
def prefix = task.ext.prefix ?: "${meta.id}"
|
||
|
|
|
||
|
|
"""
|
||
|
|
echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml
|
||
|
|
sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
|
||
|
|
sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
|
||
|
|
mkdir temp
|
||
|
|
maxquant mqpar_changed.xml
|
||
|
|
mv combined/txt/*.txt .
|
||
|
|
"""
|
||
|
|
}
|