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37 lines
1,002 B
Text
37 lines
1,002 B
Text
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { NEXTGENMAP } from '../../../modules/nextgenmap/main.nf'
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//
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// Test with single-end data
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//
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workflow test_nextgenmap_single {
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input = [
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[ id:'test', single_end:true ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], 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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NEXTGENMAP ( input, fasta )
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}
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//
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// Test with paired-end data
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//
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workflow test_bwamem2_mem_paired_end {
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input = [
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[ id:'test', single_end:false ], // meta map
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[
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file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], 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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NEXTGENMAP ( input, fasta )
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}
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