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e726b1730d
* MD finally supports cram output * publish crai file * fix test output * fix mv * figure out if contains breaks stuff * remove variable checksum * add contains check * remove variable checksum Co-authored-by: Maxime U. Garcia <max.u.garcia@gmail.com>
15 lines
379 B
Text
15 lines
379 B
Text
process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: GATK4_MARKDUPLICATES {
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ext.args = '--CREATE_INDEX true'
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ext.prefix = { "${meta.id}.bam" }
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}
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withName: GATK4_MARKDUPLICATES_CRAM {
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ext.args = '--CREATE_INDEX true'
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ext.prefix = { "${meta.id}.cram" }
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}
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}
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