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37 lines
1.1 KiB
Text
Generated
37 lines
1.1 KiB
Text
Generated
process BRACKEN_COMBINEBRACKENOUTPUTS {
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tag "$meta.id"
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label 'process_low'
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conda "bioconda::bracken=2.7"
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container "${ 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(input)
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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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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 ?: "${meta.id}"
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// WARN: Version information not provided by tool on CLI.
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// Please update version string below when bumping container versions.
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def VERSION = '2.7'
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"""
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combine_bracken_outputs.py \\
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$args \\
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--files ${input} \\
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-o ${prefix}.txt
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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combine_bracken_output: ${VERSION}
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END_VERSIONS
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"""
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}
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