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41 lines
1.1 KiB
Text
41 lines
1.1 KiB
Text
process DAMAGEPROFILER {
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tag "$meta.id"
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label 'process_low'
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conda (params.enable_conda ? "bioconda::damageprofiler=1.1" : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/damageprofiler:1.1--hdfd78af_2' :
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'quay.io/biocontainers/damageprofiler:1.1--hdfd78af_2' }"
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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 fai
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path specieslist
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output:
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tuple val(meta), path("${prefix}"), emit: results
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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def reference = fasta ? "-r $fasta" : ""
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def species_list = specieslist ? "-sf $specieslist" : ""
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"""
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damageprofiler \\
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-i $bam \\
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-o $prefix/ \\
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$args \\
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$reference \\
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$species_list
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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damageprofiler: \$(damageprofiler -v | sed 's/^DamageProfiler v//')
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END_VERSIONS
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"""
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}
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