#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { BWAMETH_INDEX                     } from '../../../../modules/bwameth/index/main.nf' addParams( options: [:]                               )
include { BWAMETH_ALIGN as BWAMETH_ALIGN_SE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_single_end' ] )
include { BWAMETH_ALIGN as BWAMETH_ALIGN_PE } from '../../../../modules/bwameth/align/main.nf' addParams( options: [ publish_dir:'test_paired_end' ] )

//
// Test with single-end data
//
workflow test_bwameth_align_single_end {
    input = [ [ id:'test', single_end:true ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true) ]
            ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

    BWAMETH_INDEX ( fasta )
    BWAMETH_ALIGN_SE ( input, BWAMETH_INDEX.out.index )
}

//
// Test with paired-end data
//
workflow test_bwameth_align_paired_end {
    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['sarscov2']['illumina']['test_methylated_1_fastq_gz'], checkIfExists: true),
                file(params.test_data['sarscov2']['illumina']['test_methylated_2_fastq_gz'], checkIfExists: true) ]
            ]
    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)

    BWAMETH_INDEX ( fasta )
    BWAMETH_ALIGN_PE ( input, BWAMETH_INDEX.out.index )
}