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44 lines
1.2 KiB
Text
44 lines
1.2 KiB
Text
process ELPREP_MERGE {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::elprep=5.1.2" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/elprep:5.1.2--he881be0_0':
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'quay.io/biocontainers/elprep:5.1.2--he881be0_0' }"
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input:
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("**.{bam,sam}"), emit: bam
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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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if (meta.single_end) {
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args += " --single-end"
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}
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def suffix = args.contains("--output-type sam") ? "sam" : "bam"
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"""
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# create directory and move all input so elprep can find and merge them before splitting
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mkdir input
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mv ${bam} input/
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elprep merge \\
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input \\
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${prefix}.${suffix} \\
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$args \\
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--nr-of-threads $task.cpus
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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elprep: \$(elprep 2>&1 | head -n2 | tail -n1 |sed 's/^.*version //;s/ compiled.*\$//')
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END_VERSIONS
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"""
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}
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