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https://github.com/MillironX/nf-core_modules.git
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41 lines
1.6 KiB
Text
41 lines
1.6 KiB
Text
process SEACR_CALLPEAK {
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tag "$meta.id"
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label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.30.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' :
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'quay.io/biocontainers/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:f4bb19b68e66de27e4c64306f951d5ff11919931-0' }"
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input:
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tuple val(meta), path(bedgraph), path(ctrlbedgraph)
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val (threshold)
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output:
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tuple val(meta), path("*.bed"), emit: bed
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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 ?: "${meta.id}"
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def function_switch = ctrlbedgraph ? "$ctrlbedgraph" : "$threshold"
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def VERSION = '1.3' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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SEACR_1.3.sh \\
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$bedgraph \\
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$function_switch \\
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$args \\
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$prefix
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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seacr: $VERSION
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bedtools: \$(bedtools --version | sed -e "s/bedtools v//g")
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r-base: \$(echo \$(R --version 2>&1) | sed 's/^.*R version //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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