nf-core_modules/tests/modules/bwa/mem/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../modules/bwa/index/main.nf' addParams( options: [:] )
include { BWA_MEM } from '../../../../modules/bwa/mem/main.nf' addParams( options: [:] )
//
// Test with single-end data
//
workflow test_bwa_mem_single_end {
input = [ [ id:'test', single_end:true ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index )
}
//
// Test with paired-end data
//
workflow test_bwa_mem_paired_end {
input = [ [ id:'test', single_end:false ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true) ]
]
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
BWA_INDEX ( fasta )
BWA_MEM ( input, BWA_INDEX.out.index )
}