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4e5b6ed843
* Fix picard/markduplicates with new options syntax * Delete md5sum for bam files and add contains for metrics.txt Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
22 lines
911 B
Text
22 lines
911 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { PICARD_MARKDUPLICATES } from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [:] )
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include { PICARD_MARKDUPLICATES as PICARD_MARKDUPLICATES_UNSORTED} from '../../../../modules/picard/markduplicates/main.nf' addParams( options: [args : 'ASSUME_SORT_ORDER=queryname' ] )
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workflow test_picard_markduplicates_sorted_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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]
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PICARD_MARKDUPLICATES ( input )
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}
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workflow test_picard_markduplicates_unsorted_bam {
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input = [ [ id:'test', single_end:false ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
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]
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PICARD_MARKDUPLICATES_UNSORTED ( input )
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}
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