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38 lines
1.1 KiB
Text
38 lines
1.1 KiB
Text
process RACON {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::racon=1.4.20" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/racon:1.4.20--h9a82719_1' :
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'quay.io/biocontainers/racon:1.4.20--h9a82719_1' }"
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input:
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tuple val(meta), path(reads), path(assembly), path(paf)
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output:
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tuple val(meta), path('*_assembly_consensus.fasta.gz') , emit: improved_assembly
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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 ?: "${meta.id}"
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"""
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racon -t "$task.cpus" \\
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"${reads}" \\
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"${paf}" \\
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$args \\
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"${assembly}" > \\
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${prefix}_assembly_consensus.fasta
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gzip -n ${prefix}_assembly_consensus.fasta
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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racon: \$( racon --version 2>&1 | sed 's/^.*v//' )
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END_VERSIONS
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"""
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}
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