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https://github.com/MillironX/nf-core_modules.git
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d1c6082a66
* Update HISAT2 build module * Bump preseq version * Fix tests * Add meta.yml for preseq to fix linting * Auto-detect --genomeSAindexNbases for smaller genomes * Add placeholder to use human data for the tests * Add CSI output option to samtools/index * Fix samtools/index tests
45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName } from './functions'
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params.options = [:]
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options = initOptions(params.options)
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process PRESEQ_LCEXTRAP {
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tag "$meta.id"
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label 'process_medium'
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label 'error_ignore'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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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)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/preseq:3.1.2--h06ef8b0_1"
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} else {
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container "quay.io/biocontainers/preseq:3.1.2--h06ef8b0_1"
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}
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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("*.ccurve.txt"), emit: ccurve
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tuple val(meta), path("*.log") , emit: log
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def paired_end = meta.single_end ? '' : '-pe'
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"""
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preseq \\
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lc_extrap \\
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$options.args \\
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$paired_end \\
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-output ${prefix}.ccurve.txt \\
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$bam
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cp .command.err ${prefix}.command.log
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echo \$(preseq 2>&1) | sed 's/^.*Version: //; s/Usage:.*\$//' > ${software}.version.txt
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"""
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}
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