nf-core_modules/tests/modules/bwamem2/mem/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* Update README

* Rename pytest_software.yml to pytest_modules.yml

* Rename main software directory to modules

* Remove deprecated modules

* Rename tests software to modules

* Replace paths for tests in pytest_modules.yml

* Replace software with modules in Github Actions

* Replace software with modules in main.nf tests

* Rename software to modules in test.yml
2021-07-07 10:10:18 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { BWAMEM2_INDEX } from '../../../../modules/bwamem2/index/main.nf' addParams( options: [:] )
include { BWAMEM2_MEM } from '../../../../modules/bwamem2/mem/main.nf' addParams( options: [:] )
//
// Test with single-end data
//
workflow test_bwamem2_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)
BWAMEM2_INDEX ( fasta )
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
}
//
// Test with paired-end data
//
workflow test_bwamem2_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)
BWAMEM2_INDEX ( fasta )
BWAMEM2_MEM ( input, BWAMEM2_INDEX.out.index )
}