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38 lines
1 KiB
Text
38 lines
1 KiB
Text
process SCOARY {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::scoary=1.6.16" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/scoary:1.6.16--py_2' :
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'quay.io/biocontainers/scoary:1.6.16--py_2' }"
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input:
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tuple val(meta), path(genes), path(traits)
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path(tree)
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output:
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tuple val(meta), path("*.csv"), emit: csv
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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 newick_tree = tree ? "-n ${tree}" : ""
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"""
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scoary \\
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$args \\
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--no-time \\
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--threads $task.cpus \\
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--traits $traits \\
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--genes $genes
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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scoary: \$( scoary --version 2>&1 )
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END_VERSIONS
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"""
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}
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