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5320ab7e6c
* Fix kleborate inputs * Update test.yml Co-authored-by: Sébastien Guizard <sguizard@ed.ac.uk>
31 lines
931 B
Text
31 lines
931 B
Text
process KLEBORATE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::kleborate=2.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kleborate:2.1.0--pyhdfd78af_1' :
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'quay.io/biocontainers/kleborate:2.1.0--pyhdfd78af_1' }"
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input:
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tuple val(meta), path(fastas)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml" , emit: versions
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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kleborate \\
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$args \\
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--outfile ${prefix}.results.txt \\
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--assemblies $fastas
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kleborate: \$( echo \$(kleborate --version | sed 's/Kleborate v//;'))
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END_VERSIONS
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"""
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}
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