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45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
process BWA_MEM {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bwa=0.7.17 bioconda::samtools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' :
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'quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:c56a3aabc8d64e52d5b9da1e8ecec2031668596d-0' }"
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input:
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tuple val(meta), path(reads)
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path index
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val sort_bam
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output:
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tuple val(meta), path("*.bam"), emit: bam
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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def args2 = task.ext.args2 ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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def read_group = meta.read_group ? "-R ${meta.read_group}" : ""
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def samtools_command = sort_bam ? 'sort' : 'view'
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa mem \\
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$args \\
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$read_group \\
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-t $task.cpus \\
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\$INDEX \\
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$reads \\
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| samtools $samtools_command $args2 --threads $task.cpus -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwa: \$(echo \$(bwa 2>&1) | sed 's/^.*Version: //; s/Contact:.*\$//')
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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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