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33 lines
1.1 KiB
Text
33 lines
1.1 KiB
Text
process CENTRIFUGE_KREPORT {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::centrifuge=1.0.4_beta" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/centrifuge:1.0.4_beta--h9a82719_6':
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'quay.io/biocontainers/centrifuge:1.0.4_beta--h9a82719_6' }"
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input:
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tuple val(meta), path(results)
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path db
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output:
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tuple val(meta), path('*.txt') , emit: kreport
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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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db_name=`find -L ${db} -name "*.1.cf" -not -name "._*" | sed 's/.1.cf//'`
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centrifuge-kreport -x \$db_name ${results} > ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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centrifuge: \$( centrifuge --version | sed -n 1p | sed 's/^.*centrifuge-class version //')
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END_VERSIONS
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"""
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}
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