#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { CENTRIFUGE } from '../../../modules/centrifuge/main.nf'

workflow test_centrifuge_single_end {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
            ]
    db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
    save_unaligned = true
    save_aligned = false
    sam_format = false

    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )

}

workflow test_centrifuge_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) ]
            ]
     db   =  file("https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/delete_me/minigut_cf.tar.gz", checkIfExists: true)
     save_unaligned = true
     save_aligned = false
     sam_format = false

    CENTRIFUGE ( input, db, save_unaligned, save_aligned, sam_format )


}