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37 lines
1 KiB
Text
37 lines
1 KiB
Text
process MERYL_COUNT {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::meryl=1.3" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
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'quay.io/biocontainers/meryl:1.3--h87f3376_1' }"
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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("*.meryldb"), emit: meryl_db
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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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for READ in $reads; do
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meryl count \\
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threads=$task.cpus \\
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$args \\
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$reads \\
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output read.\${READ%.f*}.meryldb
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done
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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meryl: \$( meryl --version |& sed 's/meryl //' )
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END_VERSIONS
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"""
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}
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