#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GATK_REALIGNERTARGETCREATOR } from '../../../../modules/gatk/realignertargetcreator/main.nf'
include { GATK_INDELREALIGNER } from '../../../../modules/gatk/indelrealigner/main.nf'


workflow test_gatk_indelrealigner {


    fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
    fai   = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
    dict  = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)

    input_realignertargetcreator     = [ [ id:'test' ], // meta map
                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
                ]

    GATK_REALIGNERTARGETCREATOR ( input_realignertargetcreator, fasta, fai, dict, [] )

    ch_intervals = GATK_REALIGNERTARGETCREATOR.out.intervals

    ch_bams_indelrealigner = Channel.of([ [ id:'test' ], // meta map
                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
                  file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
                ])

    ch_input_indelrealigner = ch_bams_indelrealigner.mix(ch_intervals).groupTuple(by: 0).map{ [it[0], it[1][0], it[2], it[1][1] ] }.dump(tag: "input")

    GATK_INDELREALIGNER ( ch_input_indelrealigner, fasta, fai, dict, [] )
}