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0337916f8a
* Initial work on yara module * Adding in index basics * Updated the index stuff * Adding in proper tests * Fix editorconfig * Odd paths * that should do it * Fix tests * Fix tests * FFS * Once more * Mapping is not deterministic
48 lines
1.9 KiB
Text
48 lines
1.9 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 YARA_MAPPER {
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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), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::yara=1.0.2 bioconda::samtools=1.12" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0"
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} else {
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container "quay.io/biocontainers/mulled-v2-f13549097a0d1ca36f9d4f017636fb3609f6c083:f794a548b8692f29264c8984ff116c2141b90d9e-0"
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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("*.mapped.bam"), emit: 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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if(meta.single_end) {
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"""
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yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara $reads | samtools view -@ ${task.cpus} -hb -F4 > ${prefix}.mapped.bam
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echo \$(yara_mapper --help 2>&1) > ${software}.version.txt
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"""
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} else {
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"""
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yara_mapper $options.args -t ${task.cpus} -f bam ${index}/yara ${reads[0]} ${reads[1]} > output.bam
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samtools view -@ ${task.cpus} -hF 4 -f 0x40 -b output.bam > ${prefix}_1.mapped.bam
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samtools view -@ ${task.cpus} -hF 4 -f 0x80 -b output.bam > ${prefix}_2.mapped.bam
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echo \$(yara_mapper --version 2>&1) | grep -e "yara_mapper version:" | sed 's/yara_mapper version: //g' > ${software}.version.txt
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"""
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}
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}
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