process MAXQUANT_LFQ { tag "$meta.id" label 'process_long' conda (params.enable_conda ? "bioconda::maxquant=2.0.3.0=py310hdfd78af_1" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/maxquant:2.0.3.0--py310hdfd78af_1" } else { container "quay.io/biocontainers/maxquant:2.0.3.0--py310hdfd78af_1" } input: tuple val(meta), path(fasta), path(paramfile) path raw output: tuple val(meta), path("*.txt"), emit: maxquant_txt path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" """ cat <<-END_VERSIONS > versions.yml "${task.process}": maxquant: \$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") END_VERSIONS sed \"s_.*_$task.cpus_\" ${paramfile} > mqpar_changed.xml sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml mkdir temp maxquant mqpar_changed.xml mv combined/txt/*.txt . """ }