nf-core_modules/modules/preseq/lcextrap/main.nf

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// Import generic module functions
include { initOptions; saveFiles; getSoftwareName; getProcessName } from './functions'
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params.options = [:]
options = initOptions(params.options)
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process PRESEQ_LCEXTRAP {
tag "$meta.id"
label 'process_medium'
label 'error_ignore'
publishDir "${params.outdir}",
mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), meta:meta, publish_by_meta:['id']) }
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conda (params.enable_conda ? "bioconda::preseq=3.1.2" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1"
} else {
container "quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1"
}
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input:
tuple val(meta), path(bam)
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output:
tuple val(meta), path("*.ccurve.txt"), emit: ccurve
tuple val(meta), path("*.log") , emit: log
path "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
"""
preseq \\
lc_extrap \\
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$options.args \\
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$paired_end \\
-output ${prefix}.ccurve.txt \\
$bam
cp .command.err ${prefix}.command.log
cat <<-END_VERSIONS > versions.yml
${getProcessName(task.process)}:
${getSoftwareName(task.process)}: \$(echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//')
END_VERSIONS
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"""
}