nf-core_modules/modules/deeptools/computematrix/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process DEEPTOOLS_COMPUTEMATRIX {
tag "$meta.id"
label 'process_high'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
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::deeptools=3.5.1' : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0"
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} else {
container "quay.io/biocontainers/deeptools:3.5.1--py_0"
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}
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input:
tuple val(meta), path(bigwig)
path bed
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output:
tuple val(meta), path("*.mat.gz") , emit: matrix
tuple val(meta), path("*.mat.tab"), emit: table
path "versions.yml" , emit: versions
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script:
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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"""
computeMatrix \\
$options.args \\
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--regionsFileName $bed \\
--scoreFileName $bigwig \\
--outFileName ${prefix}.computeMatrix.mat.gz \\
--outFileNameMatrix ${prefix}.computeMatrix.vals.mat.tab \\
--numberOfProcessors $task.cpus
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(computeMatrix --version | sed -e "s/computeMatrix //g")
END_VERSIONS
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"""
}