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f3ffa69b8d
* feat(dragmap): Add initial hastable module * feat(dragmap): Add initial align module * test(dragmap): Remove md5sum Forgot sam files have a header. Might pipe this through samtools. * build(dragmap): Add mulled container * chore(dragmap): Update prefix * feat(dragmap): Output a bam file * feat(dragmap): Add log files * Update modules/dragmap/align/meta.yml Co-authored-by: Jose Espinosa-Carrasco <kadomu@gmail.com>
59 lines
2.1 KiB
Text
59 lines
2.1 KiB
Text
process DRAGMAP_ALIGN {
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tag "$meta.id"
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label 'process_high'
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conda (params.enable_conda ? "bioconda::dragmap=1.2.1 bioconda::samtools=1.14 conda-forge::pigz=2.3.4" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0':
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'quay.io/biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:f7aad9060cde739c95685fc5ff6d6f7e3ec629c8-0' }"
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input:
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tuple val(meta), path(reads)
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path hashmap
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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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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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if (meta.single_end) {
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"""
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dragen-os \\
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-r $hashmap \\
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-1 $reads \\
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--num-threads $task.cpus \\
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$args \\
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2> ${prefix}.dragmap.log \\
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| samtools view -@ $task.cpus $args2 -bhS -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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} else {
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"""
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dragen-os \\
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-r $hashmap \\
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-1 ${reads[0]} \\
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-2 ${reads[1]} \\
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--num-threads $task.cpus \\
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$args \\
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2> ${prefix}.dragmap.log \\
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| samtools view -@ $task.cpus $args2 -bhS -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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}
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