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42 lines
1.2 KiB
Text
42 lines
1.2 KiB
Text
process ARRIBA {
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tag "$meta.id"
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label 'process_medium'
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conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
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'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
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input:
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tuple val(meta), path(bam)
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path fasta
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path gtf
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output:
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tuple val(meta), path("*.fusions.tsv") , emit: fusions
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tuple val(meta), path("*.fusions.discarded.tsv"), emit: fusions_fail
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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 blacklist = (args.contains('-b')) ? '' : '-f blacklist'
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"""
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arriba \\
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-x $bam \\
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-a $fasta \\
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-g $gtf \\
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-o ${prefix}.fusions.tsv \\
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-O ${prefix}.fusions.discarded.tsv \\
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$blacklist \\
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$args
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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arriba: \$(arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s//')
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END_VERSIONS
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"""
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}
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