#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'

workflow test_expansionhunter {

    input = [ [ id:'test', gender:'male' ], // meta map
              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
              file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
            ]
    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
    variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)

    EXPANSIONHUNTER ( input, fasta, variant_catalog )
}