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42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process FGBIO_FASTQTOBAM {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::fgbio=1.4.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/fgbio:1.4.0--hdfd78af_0' :
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'quay.io/biocontainers/fgbio:1.4.0--hdfd78af_0' }"
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input:
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tuple val(meta), path(reads)
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val read_structure
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output:
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tuple val(meta), path("*_umi_converted.bam"), emit: umibam
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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 prefix = task.ext.prefix ?: "${meta.id}"
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"""
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mkdir tmp
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fgbio \\
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--tmp-dir=${PWD}/tmp \\
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FastqToBam \\
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-i $reads \\
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-o "${prefix}_umi_converted.bam" \\
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--read-structures $read_structure \\
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--sample $meta.id \\
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--library $meta.id \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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fgbio: \$( echo \$(fgbio --version 2>&1 | tr -d '[:cntrl:]' ) | sed -e 's/^.*Version: //;s/\\[.*\$//')
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END_VERSIONS
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"""
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}
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