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45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
process PBCCS {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::pbccs=6.2.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/pbccs:6.2.0--h9ee0642_0' :
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'quay.io/biocontainers/pbccs:6.2.0--h9ee0642_0' }"
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input:
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tuple val(meta), path(bam), path(pbi)
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val chunk_num
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val chunk_on
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output:
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tuple val(meta), path("*.chunk*.bam") , emit: bam
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tuple val(meta), path("*.chunk*.bam.pbi") , emit: pbi
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tuple val(meta), path("*.report.txt" ) , emit: report_txt
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tuple val(meta), path("*.report.json" ) , emit: report_json
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tuple val(meta), path("*.metrics.json.gz"), emit: metrics
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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 ?: "${meta.id}"
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"""
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ccs \\
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$bam \\
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${prefix}.chunk${chunk_num}.bam \\
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--report-file ${prefix}.chunk${chunk_num}.report.txt \\
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--report-json ${prefix}.chunk${chunk_num}.report.json \\
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--metrics-json ${prefix}.chunk${chunk_num}.metrics.json.gz \\
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--chunk $chunk_num/$chunk_on \\
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-j $task.cpus \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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pbccs: \$(echo \$(ccs --version 2>&1) | grep 'ccs' | sed 's/^.*ccs //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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