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veitveit 2022-02-08 09:50:33 +01:00
parent 34dc4c181d
commit ad98111756
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modules/maxquant/lfq/#main.nf#
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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 .
"""
}