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45dee96bdf
* Specify more guidelines on input channels * Linting * Updates based on code review * Update README.md * Fix broken sentence * Add bwa/aln module * Also output reads as required with SAI * fix container paths * Sync bwa version samese/sampe * Apply suggestions from code review Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
67 lines
2 KiB
Text
67 lines
2 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 BWA_ALN {
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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::bwa=0.7.17" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bwa:0.7.17--h5bf99c6_8"
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} else {
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container "quay.io/biocontainers/bwa:0.7.17--h5bf99c6_8"
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}
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input:
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tuple val(meta), path(reads)
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path index
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output:
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tuple val(meta), path(reads), path("*.sai"), emit: sai
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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}" : "${meta.id}"
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if (meta.single_end) {
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa aln \\
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$options.args \\
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-t $task.cpus \\
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-f ${prefix}.sai \\
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\$INDEX \\
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${reads}
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echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
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"""
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} else {
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa aln \\
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$options.args \\
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-t $task.cpus \\
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-f ${prefix}.1.sai \\
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\$INDEX \\
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${reads[0]}
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bwa aln \\
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$options.args \\
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-t $task.cpus \\
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-f ${prefix}.2.sai \\
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\$INDEX \\
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${reads[1]}
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echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//' > ${software}.version.txt
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"""
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}
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}
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