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41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
process HOMER_ANNOTATEPEAKS {
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tag "$meta.id"
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label 'process_medium'
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// WARN: Version information not provided by tool on CLI. Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::homer=4.11" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/homer:4.11--pl526hc9558a2_3' :
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'quay.io/biocontainers/homer:4.11--pl526hc9558a2_3' }"
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input:
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tuple val(meta), path(peak)
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path fasta
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path gtf
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output:
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tuple val(meta), path("*annotatePeaks.txt"), emit: txt
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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 ?: "${meta.id}"
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def VERSION = '4.11' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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annotatePeaks.pl \\
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$peak \\
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$fasta \\
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$args \\
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-gtf $gtf \\
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-cpu $task.cpus \\
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> ${prefix}.annotatePeaks.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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homer: $VERSION
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END_VERSIONS
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"""
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}
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