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41 lines
1.3 KiB
Text
41 lines
1.3 KiB
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { BCFTOOLS_REHEADER } from '../../../../modules/bcftools/reheader/main.nf' addParams( options: [suffix: '.updated'] )
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workflow test_bcftools_reheader_update_sequences {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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header = []
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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workflow test_bcftools_reheader_new_header {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = []
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header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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workflow test_bcftools_reheader_new_header_update_sequences {
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input = [
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[ id:'test', single_end:false ],
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true)
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]
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fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
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header = file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
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BCFTOOLS_REHEADER ( input, fai, header )
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}
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