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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process GAPPA_EXAMINEGRAFT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::gappa=0.8.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/gappa:0.8.0--h9a82719_0':
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'quay.io/biocontainers/gappa:0.8.0--h9a82719_0' }"
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input:
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tuple val(meta), path(jplace)
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output:
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tuple val(meta), path("*.newick"), emit: newick
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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 ?: "${meta.id}"
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"""
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gappa \\
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examine \\
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graft \\
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$args \\
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--threads $task.cpus \\
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--file-prefix ${prefix}. \\
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--jplace-path $jplace
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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gappa: \$(echo \$(gappa --version 2>&1 | sed 's/v//' ))
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END_VERSIONS
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"""
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}
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