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69 lines
2 KiB
Text
69 lines
2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
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include { UNTAR } from '../../../modules/untar/main.nf'
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workflow test_rtgtools_vcfeval {
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input = [
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[ id:'test' ], // meta map
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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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]
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truth = [
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
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]
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truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
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evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
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compressed_sdf = [
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[],
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file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
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]
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sdf = UNTAR( compressed_sdf ).untar
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.map({
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meta, folder ->
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folder
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})
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}
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workflow test_rtgtools_vcfeval_no_optional_inputs {
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input = [
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[ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
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[],
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]
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truth = [
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file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
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[]
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]
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truth_regions = []
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evaluation_regions = []
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compressed_sdf = [
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[],
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file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
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]
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sdf = UNTAR( compressed_sdf ).untar
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.map({
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meta, folder ->
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[folder]
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})
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RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
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}
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