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45 lines
1.5 KiB
Text
45 lines
1.5 KiB
Text
process UMITOOLS_DEDUP {
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tag "$meta.id"
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label "process_medium"
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conda (params.enable_conda ? "bioconda::umi_tools=1.1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/umi_tools:1.1.2--py38h4a8c8d9_0' :
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'quay.io/biocontainers/umi_tools:1.1.2--py38h4a8c8d9_0' }"
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input:
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tuple val(meta), path(bam), path(bai)
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val get_output_stats
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output:
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tuple val(meta), path("*.bam") , emit: bam
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tuple val(meta), path("*edit_distance.tsv"), optional:true, emit: tsv_edit_distance
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tuple val(meta), path("*per_umi.tsv") , optional:true, emit: tsv_per_umi
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tuple val(meta), path("*per_position.tsv") , optional:true, emit: tsv_umi_per_position
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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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def paired = meta.single_end ? "" : "--paired"
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def stats = get_output_stats ? "--output-stats $prefix" : ""
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if (!(args ==~ /.*--random-seed.*/)) {args += " --random-seed=100"}
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"""
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PYTHONHASHSEED=0 umi_tools \\
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dedup \\
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-I $bam \\
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-S ${prefix}.bam \\
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$stats \\
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$paired \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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umitools: \$(umi_tools --version 2>&1 | sed 's/^.*UMI-tools version://; s/ *\$//')
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END_VERSIONS
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"""
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}
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