#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
include { UNTAR }        from '../../../modules/untar/main.nf'
workflow test_controlfreec {

    input = [
        [ id:'test', single_end:false, sex:'XX' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], checkIfExists: true),
        [],[],[],[]
    ]

    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)

    dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
    dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)

    chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
    target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)

    UNTAR(chrfiles)
    CONTROLFREEC (  input,
                            fasta,
                            fai,
                            [],
                            dbsnp,
                            dbsnp_tbi,
                            UNTAR.out.untar,
                            [],
                            target_bed,
                            []
                        )
}