#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { GATK4_COMBINEGVCFS } from '../../../../modules/gatk4/combinegvcfs/main.nf'

workflow test_gatk4_combinegvcfs {
    
    input = [ [ id:'test', single_end:false ], // meta map
              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf'], checkIfExists: true) ],
              [ file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf_idx'], checkIfExists: true),
                file(params.test_data['homo_sapiens']['illumina']['test2_genome_vcf_idx'], checkIfExists: true) ]              
           ]

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

    fasta_fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)

    fasta_dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)       

    GATK4_COMBINEGVCFS ( input, fasta, fasta_fai, fasta_dict )
}