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36 lines
1.5 KiB
Text
36 lines
1.5 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { GATK4_LEFTALIGNANDTRIMVARIANTS } from '../../../../modules/gatk4/leftalignandtrimvariants/main.nf'
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workflow test_gatk4_leftalignandtrimvariants_interval {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
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file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true),
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
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}
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workflow test_gatk4_leftalignandtrimvariants_no_interval {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
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[]
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
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GATK4_LEFTALIGNANDTRIMVARIANTS ( input, fasta, fai, dict )
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}
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