#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { VARDICTJAVA } from '../../../modules/vardictjava/main.nf'

workflow test_vardictjava {
    
    bam_input_ch = Channel.value([
        [ id:'test' ], // 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)
    ])

    bed = Channel.value(file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true))

    reference = Channel.value([
        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
    ])

    VARDICTJAVA ( bam_input_ch, bed, reference )
}