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42 lines
1.2 KiB
Plaintext
42 lines
1.2 KiB
Plaintext
process KAIJU_KAIJU {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::kaiju=1.8.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
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'quay.io/biocontainers/kaiju:1.8.2--h5b5514e_1' }"
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input:
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tuple val(meta), path(reads)
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path(db)
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output:
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tuple val(meta), path('*.tsv'), emit: results
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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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def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
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"""
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dbnodes=`find -L ${db} -name "*nodes.dmp"`
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dbname=`find -L ${db} -name "*.fmi" -not -name "._*"`
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kaiju \\
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$args \\
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-z $task.cpus \\
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-t \$dbnodes \\
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-f \$dbname \\
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-o ${prefix}.tsv \\
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$input
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
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END_VERSIONS
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"""
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}
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