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33 lines
1.2 KiB
Text
33 lines
1.2 KiB
Text
process MAXQUANT_LFQ {
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tag "$meta.id"
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label 'process_long'
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conda (params.enable_conda ? "bioconda::maxquant=2.0.1.0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
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} else {
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container "wombatp/maxquant-pipeline:v0.13"
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}
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input:
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tuple val(meta), path(fasta), path(paramfile)
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path raw
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output:
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tuple val(meta), path("*.txt"), emit: maxquant_txt
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path "versions.yml" , emit: version
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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export PATH=/usr/local/lib/dotnet:/usr/local/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/bin:/opt/conda/envs/nf-core-maxquant/lib/dotnet/tools:/opt/conda/envs/nf-core-maxquant/lib/dotnet:$PATH
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echo \"maxquant: \"\$(maxquant --version 2>&1 > /dev/null | cut -f2 -d\" \") > versions.yml
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sed \"s_<numThreads>.*_<numThreads>$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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