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34 lines
1 KiB
Text
Generated
34 lines
1 KiB
Text
Generated
process KRAKENTOOLS_COMBINEKREPORTS {
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label 'process_single'
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conda "bioconda::krakentools=1.2"
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/krakentools:1.2--pyh5e36f6f_0':
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'quay.io/biocontainers/krakentools:1.2--pyh5e36f6f_0' }"
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input:
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tuple val(meta), path(kreports)
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output:
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tuple val(meta), path("*.txt"), emit: txt
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path "versions.yml", emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def VERSION = '1.2' // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions.
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"""
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combine_kreports.py \\
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-r ${kreports} \\
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-o ${prefix}.txt \\
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${args}
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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combine_kreports.py: ${VERSION}
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END_VERSIONS
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"""
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}
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