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07e2868920
* When the `-i` option of bgzip is given, an index is created and needs to be considered an output * It is not necessary to use a subfolder * Updated meta.yml too * Also check that an index name hasn't been requested Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
39 lines
1.4 KiB
Text
39 lines
1.4 KiB
Text
process TABIX_BGZIP {
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tag "$meta.id"
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label 'process_single'
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conda (params.enable_conda ? 'bioconda::tabix=1.11' : null)
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container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
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'https://depot.galaxyproject.org/singularity/tabix:1.11--hdfd78af_0' :
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'quay.io/biocontainers/tabix:1.11--hdfd78af_0' }"
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input:
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tuple val(meta), path(input)
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output:
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tuple val(meta), path("${prefix}*"), emit: output
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tuple val(meta), path("*gzi") , emit: gzi, optional: true
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path "versions.yml" , emit: versions
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when:
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task.ext.when == null || task.ext.when
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script:
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def args = task.ext.args ?: ''
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prefix = task.ext.prefix ?: "${meta.id}"
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in_bgzip = input.toString().endsWith(".gz")
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command1 = in_bgzip ? '-d' : '-c'
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command2 = in_bgzip ? '' : " > ${prefix}.${input.getExtension()}.gz"
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// Name the index according to $prefix, unless a name has been requested
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if ((args.matches("(^| )-i\\b") || args.matches("(^| )--index(\$| )")) && !args.matches("(^| )-I\\b") && !args.matches("(^| )--index-name\\b")) {
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args = args + " -I ${prefix}.${input.getExtension()}.gz.gzi"
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}
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"""
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bgzip $command1 $args -@${task.cpus} $input $command2
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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tabix: \$(echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/ .*\$//')
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END_VERSIONS
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"""
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}
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