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https://github.com/MillironX/nf-core_modules.git
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49b18b1639
* add stub section * add stub for bcftools norm * add stub to more modules * fix expansionhunter tests * revert changes -picard * Update stub to write version no.s to a file * add picard * revert picard again * add stubs to more modules * fix bwamem2 * add bcftools view * add stubs * fix svdb query * review suggestions
57 lines
1.9 KiB
Text
57 lines
1.9 KiB
Text
process BWAMEM2_MEM {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::bwa-mem2=2.2.1 bioconda::samtools=1.15" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' :
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'quay.io/biocontainers/mulled-v2-e5d375990341c5aef3c9aff74f96f66f65375ef6:8ee25ae85d7a2bacac3e3139db209aff3d605a18-0' }"
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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 ${meta.read_group}" : ""
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def samtools_command = sort_bam ? 'sort' : 'view'
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"""
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INDEX=`find -L ./ -name "*.amb" | sed 's/.amb//'`
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bwa-mem2 \\
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mem \\
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$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 -@ $task.cpus -o ${prefix}.bam -
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed '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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stub:
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def prefix = task.ext.prefix ?: "${meta.id}"
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"""
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touch ${prefix}.bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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bwamem2: \$(echo \$(bwa-mem2 version 2>&1) | sed '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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