#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { SPADES } from '../../../software/spades/main.nf' addParams( spades_hmm: false ,options: [:] )

workflow test_spades_single_end {

    def input = []
    def hmm = []
    def coronaspades = false
    input = [ [ id:'test', single_end:true ], // meta map
              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true) ] ]

    SPADES ( input, hmm, coronaspades )
}

workflow test_spades_paired_end {

    def input = []
    def hmm = []
    def coronaspades = false
    input = [ [ id:'test', single_end:false ], // meta map
              [ file("${launchDir}/tests/data/generic/fastq/test_R1.fastq.gz", checkIfExists: true),
                file("${launchDir}/tests/data/generic/fastq/test_R2.fastq.gz", checkIfExists: true) ] ]

    SPADES ( input, hmm, coronaspades )
}

workflow test_coronospades_single_end {

    def input = []
    input = [ [ id:'test', single_end:true ], // meta map
              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true) ] ]
    def hmm = []
    def coronaspades = true

    SPADES ( input, hmm, coronaspades )
}

workflow test_coronospades_paired_end {

    def input = []
    def hmm = []
    def coronaspades = true
    input = [ [ id:'test', single_end:false ], // meta map
              [ file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_1.fastq.gz", checkIfExists: true),
                file("${launchDir}/tests/data/genomics/sarscov2/fastq/test_2.fastq.gz", checkIfExists: true) ] ]

    SPADES ( input, hmm, coronaspades )
}