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23 lines
685 B
Text
23 lines
685 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'
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// TODO add REalignerTargetCrator
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workflow test_gatk_indelrealigner {
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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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file(params.test_data['sarscov2']['illumina']['test_paired_end_bai'], checkIfExists: true),
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GATK_REALIGNERTARGETCREATOR.out.intervals
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]
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reference = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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GATK_INDELREALIGNER ( input, reference, [] )
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}
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