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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
process PRESEQ_LCEXTRAP {
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tag "$meta.id"
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label 'process_medium'
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label 'error_ignore'
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conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1' :
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'quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.lc_extrap.txt"), emit: lc_extrap
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tuple val(meta), path("*.log") , emit: log
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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 ?: "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
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"""
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preseq \\
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lc_extrap \\
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$args \\
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$paired_end \\
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-output ${prefix}.lc_extrap.txt \\
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$bam
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cp .command.err ${prefix}.command.log
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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preseq: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
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END_VERSIONS
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"""
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}
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