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2e619add87
* created template for `samtools/ampliconclip` (#584) * All tests passing (#584) * Linting fixed (#584) * Final linting fixed (#584) * Optional output flags moved to `input` (#584) * typo fix (#584) * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
51 lines
1.8 KiB
Text
51 lines
1.8 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 SAMTOOLS_AMPLICONCLIP {
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tag "$meta.id"
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label 'process_medium'
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publishDir "${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::samtools=1.13" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/samtools:1.13--h8c37831_0"
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} else {
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container "quay.io/biocontainers/samtools:1.13--h8c37831_0"
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}
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input:
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tuple val(meta), path(bam)
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path bed
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val save_cliprejects
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val save_clipstats
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*.clipstats.txt") , optional:true, emit: stats
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tuple val(meta), path("*.cliprejects.bam"), optional:true, emit: rejects_bam
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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 rejects = save_cliprejects ? "--rejects-file ${prefix}.cliprejects.bam" : ""
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def stats = save_clipstats ? "-f ${prefix}.clipstats.txt" : ""
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"""
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samtools \\
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ampliconclip \\
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$options.args \\
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-@ $task.cpus \\
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$rejects \\
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$stats \\
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-b $bed \\
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-o ${prefix}.bam \\
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$bam
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echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' > ${software}.version.txt
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"""
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}
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