nf-core_modules/tests/software/bwa/mem/main.nf
Jose Espinosa-Carrasco 95e02f913f
Update comments with new style (#497)
* Update comment style on functions.nf files

* Update test main.nf comments

* Add meta for ggread
2021-05-12 14:56:46 +01:00

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1.1 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWA_INDEX } from '../../../../software/bwa/index/main.nf' addParams( options: [:] )
include { BWA_MEM } from '../../../../software/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 )
}