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44 lines
1.5 KiB
Text
44 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process MAXQUANT_LFQ {
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tag "$meta.id"
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label 'process_long'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
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} else {
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# container "wombatp/maxquant-pipeline:dev"
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container "quay.io/biocontainers/maxquant:2.0.1.0
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}
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input:
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tuple val(meta), path(fasta), path(paramfile)
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path raw
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output:
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tuple val(meta), path("*.txt"), emit: maxquant_txt
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
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maxquant --version | head -n1 - > maxquant.version.txt
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sed \"s_<numThreads>.*_<numThreads>$task.cpus</numThreads>_\" ${paramfile} > mqpar_changed.xml
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sed -i \"s|PLACEHOLDER|\$PWD/|g\" mqpar_changed.xml
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mkdir temp
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maxquant mqpar_changed.xml
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mv combined/txt/*.txt .
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"""
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}
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