#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { PHYLOFLASH } from '../../../modules/phyloflash/main.nf' addParams( options: [:] )

process STUB_PHYLOFLASH_DATABASE {
    output:
    path "ref"    , emit: silva_db
    path "UniVec" , emit: univec_db

    stub:
    """
    mkdir ref
    touch UniVec
    """
}

workflow test_phyloflash_single_end {

    STUB_PHYLOFLASH_DATABASE ()
    
    input = [ 
        [ id:'test', single_end:true ], // meta map
        [ file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true) ]
    ]

    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db,  STUB_PHYLOFLASH_DATABASE.out.univec_db )
}

workflow test_phyloflash_paired_end {

    STUB_PHYLOFLASH_DATABASE ()

    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)
        ]
    ]

    PHYLOFLASH ( input, STUB_PHYLOFLASH_DATABASE.out.silva_db,  STUB_PHYLOFLASH_DATABASE.out.univec_db )
}