#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { HAPPY } from '../../../modules/happy/main.nf'

workflow test_happy_vcf {
    
    input = [
        [ id:'test' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test_genome21_indels_vcf_gz'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
    ]

    fasta = 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)
    ])

    HAPPY ( input, fasta )
}

workflow test_happy_gvcf {
    
    input = [
        [ id:'test' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test_rnaseq_vcf'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test_genome_vcf'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)        
    ]

    fasta = 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)
    ])

    HAPPY ( input, fasta )
}