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https://github.com/MillironX/nf-core_modules.git
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43 lines
1.2 KiB
Text
43 lines
1.2 KiB
Text
process FGBIO_GROUPREADSBYUMI {
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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(taggedbam)
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val(strategy)
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output:
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tuple val(meta), path("*_umi-grouped.bam") , emit: bam
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tuple val(meta), path("*_umi_histogram.txt"), emit: histogram
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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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GroupReadsByUmi \\
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-s $strategy \\
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$args \\
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-i $taggedbam \\
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-o ${prefix}_umi-grouped.bam \\
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-f ${prefix}_umi_histogram.txt
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cat <<-END_VERSIONS > versions.yml
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"${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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