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

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
include { UNTAR } from '../../../modules/untar/main.nf'
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workflow test_rtgtools_vcfeval {
input = [
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[ id:'test' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),
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]
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)
]
truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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compressed_sdf = [
[],
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file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
]
sdf = UNTAR( compressed_sdf ).untar
.map({
meta, folder ->
folder
})
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}
workflow test_rtgtools_vcfeval_no_optional_inputs {
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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),
[]
]
truth_regions = []
evaluation_regions = []
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compressed_sdf = [
[],
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file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
]
sdf = UNTAR( compressed_sdf ).untar
.map({
meta, folder ->
[folder]
})
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}