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4f5274c3de
* feat: remove reat_group which should be set up with ext.args * fix: simplify dragmap command
46 lines
1.6 KiB
Text
46 lines
1.6 KiB
Text
process DRAGMAP_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.15.1 conda-forge::pigz=2.3.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0':
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'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }"
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input:
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tuple val(meta), path(reads)
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path hashmap
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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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tuple val(meta), path('*.log'), emit: log
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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 reads_command = meta.single_end ? "-1 $reads" : "-1 ${reads[0]} -2 ${reads[1]}"
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def samtools_command = sort_bam ? 'sort' : 'view'
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"""
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dragen-os \\
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-r $hashmap \\
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$args \\
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--num-threads $task.cpus \\
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$reads_command \\
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2> ${prefix}.dragmap.log \\
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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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dragmap: \$(echo \$(dragen-os --version 2>&1))
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samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
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pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
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END_VERSIONS
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"""
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}
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