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43 lines
1.3 KiB
Plaintext
43 lines
1.3 KiB
Plaintext
process BRACKEN_BRACKEN {
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tag "$meta.id"
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label 'process_low'
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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conda (params.enable_conda ? "bioconda::bracken=2.7" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/bracken:2.7--py39hc16433a_0':
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'quay.io/biocontainers/bracken:2.7--py39hc16433a_0' }"
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input:
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tuple val(meta), path(kraken_report)
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path database
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output:
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tuple val(meta), path(bracken_report), emit: reports
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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 ?: "${meta.id}"
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bracken_report = "${prefix}.tsv"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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"""
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bracken \\
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${args} \\
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-d '${database}' \\
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-i '${kraken_report}' \\
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-o '${bracken_report}'
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bracken: ${VERSION}
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END_VERSIONS
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"""
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}
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