nf-core_modules/tests/modules/rtgtools/vcfeval/main.nf

#!/usr/bin/env nextflow

nextflow.enable.dsl = 2

include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
include { UNTAR } from '../../../modules/untar/main.nf'

workflow test_rtgtools_vcfeval {
    
    input = [
        [ id:'test' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),        
    ]

    truth = [
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
    ]

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

    compressed_sdf = [
        [],
        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
    ]

    sdf = UNTAR( compressed_sdf ).untar
        .map({
            meta, folder ->
                folder
        })
    

    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
}

workflow test_rtgtools_vcfeval_no_index {
    
    input = [
        [ id:'test' ], // meta map
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
        [],
    ]

    truth = [
        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
        []
    ]

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

    compressed_sdf = [
        [],
        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
    ]

    sdf = UNTAR( compressed_sdf ).untar
        .map({
            meta, folder ->
                [folder]
        })

    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
}