nf-core_modules/tests/modules/adapterremoval/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { ADAPTERREMOVAL } from '../../../modules/adapterremoval/main.nf' addParams( options: [:] )
workflow test_adapterremoval_single_end {
input = [ [ id:'test', single_end:true, collapse:false ], // meta map
file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
]
ADAPTERREMOVAL ( input )
}
workflow test_adapterremoval_paired_end {
input = [ [ id:'test', single_end:false, collapse: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) ]
]
ADAPTERREMOVAL ( input )
}
workflow test_adapterremoval_paired_end_collapse {
input = [ [ id:'test', single_end:false, collapse:true ], // 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) ]
]
ADAPTERREMOVAL ( input )
}