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32 lines
901 B
Text
32 lines
901 B
Text
process PAIRIX {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::pairix=0.3.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pairix:0.3.7--py36h30a8e3e_3' :
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'quay.io/biocontainers/pairix:0.3.7--py36h30a8e3e_3' }"
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input:
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tuple val(meta), path(pair)
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output:
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tuple val(meta), path(pair), path("*.px2"), emit: index
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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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"""
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pairix \\
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$args \\
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$pair
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pairix: \$(echo \$(pairix --help 2>&1) | sed 's/^.*Version: //; s/Usage.*\$//')
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END_VERSIONS
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"""
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}
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