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42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process RAVEN {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::raven-assembler=1.6.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/raven-assembler:1.6.1--h2e03b76_0' :
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'quay.io/biocontainers/raven-assembler:1.6.1--h2e03b76_0' }"
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input:
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tuple val(meta), path(reads)
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output:
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tuple val(meta), path("*.fasta.gz"), emit: fasta
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tuple val(meta), path("*.gfa.gz") , emit: gfa
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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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# run tool
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raven \\
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-t $task.cpus \\
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--graphical-fragment-assembly ${prefix}.gfa \\
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$args \\
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$reads | \\
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gzip -c > ${prefix}.fasta.gz
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# compress assembly graph
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gzip -c ${prefix}.gfa > ${prefix}.gfa.gz
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# get tool version
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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raven: \$( raven --version )
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END_VERSIONS
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"""
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}
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