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37 lines
1.1 KiB
Text
37 lines
1.1 KiB
Text
process DEEPTOOLS_BAMCOVERAGE {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::deeptools=3.5.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/deeptools:3.5.1--py_0':
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'quay.io/biocontainers/deeptools:3.5.1--py_0' }"
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input:
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tuple val(meta), path(input), path(input_index)
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output:
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tuple val(meta), path("*.bigWig") , emit: bigwig, optional: true
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tuple val(meta), path("*.bedgraph") , emit: bedgraph, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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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}.bigWig"
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"""
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bamCoverage \\
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--bam $input \\
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$args \\
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--numberOfProcessors ${task.cpus} \\
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--outFileName ${prefix}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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deeptools: \$(bamCoverage --version | sed -e "s/bamCoverage //g")
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END_VERSIONS
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"""
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}
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