mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
69 lines
2 KiB
Text
69 lines
2 KiB
Text
#!/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)
|
|
]
|
|
|
|
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)
|
|
|
|
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, truth_regions, evaluation_regions, sdf )
|
|
}
|
|
|
|
workflow test_rtgtools_vcfeval_no_optional_inputs {
|
|
|
|
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 = []
|
|
|
|
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, truth_regions, evaluation_regions, sdf )
|
|
}
|