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23 lines
769 B
Text
23 lines
769 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { SAMTOOLS_COLLATE } from '../../../../modules/samtools/collate/main.nf'
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include { SAMTOOLS_FIXMATE } from '../../../../modules/samtools/fixmate/main.nf'
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include { SAMTOOLS_SORT } from '../../../../modules/samtools/sort/main.nf'
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include { SAMTOOLS_MARKDUP } from '../../../../modules/samtools/markdup/main.nf'
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workflow test_samtools_markdup {
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input = [
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[ 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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SAMTOOLS_COLLATE ( input, [] )
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SAMTOOLS_FIXMATE ( SAMTOOLS_COLLATE.out.bam )
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SAMTOOLS_SORT ( SAMTOOLS_FIXMATE.out.bam )
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SAMTOOLS_MARKDUP ( SAMTOOLS_SORT.out.bam, [] )
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}
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