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64 lines
3.6 KiB
Text
64 lines
3.6 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
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// All other parameters MUST be provided as a string i.e. "options.args"
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// where "params.options" is a Groovy Map that MUST be provided via the addParams section of the including workflow.
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// Any parameters that need to be evaluated in the context of a particular sample
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// e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
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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/https://depot.galaxyproject.org/singularity/maxquant:2.0.1.0--py39hdfd78af_2"
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} else {
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container "quay.io/biocontainers/quay.io/biocontainers/maxquant:2.0.1.0--py39hdfd78af_2"
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}
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input:
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// TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
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// MUST be provided as an input via a Groovy Map called "meta".
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// This information may not be required in some instances e.g. indexing reference genome files:
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// https://github.com/nf-core/modules/blob/master/software/bwa/index/main.nf
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// TODO nf-core: Where applicable please provide/convert compressed files as input/output
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// e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
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tuple val(meta), path(raw), path(paramfile)
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output:
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// TODO nf-core: Named file extensions MUST be emitted for ALL output channels
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tuple val(meta), path("combined/txt/*.txt"), emit: maxquant_txt
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// TODO nf-core: List additional required output channels/values here
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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}" : "${meta.id}"
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// TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
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// If the software is unable to output a version number on the command-line then it can be manually specified
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// e.g. https://github.com/nf-core/modules/blob/master/software/homer/annotatepeaks/main.nf
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// TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "$options.args" variable
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// TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
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// using the Nextflow "task" variable e.g. "--threads $task.cpus"
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// TODO nf-core: Please replace the example samtools command below with your module's command
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// TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
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"""
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maxquant --version > maxquant.version.txt
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# Write number of threads into parameter file
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sed "s_\<numThreads\>.*_\<numThreads\>12\<\/numThreads\>_" ${paramfile}
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# Correct folder names
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sed -i "s|PLACEHOLDER|\$PWD/|g" "${paramfile}"
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mkdir temp
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maxquant ${paramfile}
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"""
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}
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