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7b3315591a
* Remove def software line * Replace version with versions in emit statement * Fix default software names
66 lines
2.6 KiB
Text
66 lines
2.6 KiB
Text
// Import generic module functions
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include { initOptions; saveFiles; getSoftwareName; getProcessName } 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), meta:meta, publish_by_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 "versions.yml" , emit: versions
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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if (meta.single_end) {
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"""
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yara_mapper \\
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$options.args \\
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-t $task.cpus \\
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-f bam \\
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${index}/yara \\
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$reads | samtools view -@ $task.cpus -hb -F4 > ${prefix}.mapped.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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} else {
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"""
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yara_mapper \\
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$options.args \\
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-t ${task.cpus} \\
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-f bam \\
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${index}/yara \\
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${reads[0]} \\
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${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 > ${prefix}_2.mapped.bam
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cat <<-END_VERSIONS > versions.yml
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${getProcessName(task.process)}:
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${getSoftwareName(task.process)}: \$(echo \$(yara_mapper --version 2>&1) | sed 's/^.*yara_mapper version: //; s/ .*\$//')
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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END_VERSIONS
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"""
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}
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}
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