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42 lines
1.4 KiB
Text
42 lines
1.4 KiB
Text
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// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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process DEEPTOOLS_COMPUTEMATRIX {
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tag "$meta.id"
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label 'process_high'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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container "quay.io/biocontainers/deeptools:3.4.3--py_0"
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//container "https://depot.galaxyproject.org/singularity/deeptools:3.4.3--py_0"
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conda (params.conda ? "bioconda::deeptools=3.4.3" : null)
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input:
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tuple val(meta), path(bigwig)
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path bed
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val options
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output:
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tuple val(meta), path("*.mat.gz"), emit: matrix
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tuple val(meta), path("*.mat.tab"), emit: table
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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 ioptions = initOptions(options)
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def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}"
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"""
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computeMatrix \\
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$ioptions.args \\
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--regionsFileName $bed \\
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--scoreFileName $bigwig \\
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--outFileName ${prefix}.computeMatrix.mat.gz \\
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--outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\
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--numberOfProcessors $task.cpus
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computeMatrix --version | sed -e "s/computeMatrix //g" > ${software}.version.txt
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"""
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}
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