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40 lines
1.2 KiB
Text
40 lines
1.2 KiB
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { RHOCALL_ANNOTATE } from '../../../../modules/rhocall/annotate/main.nf'
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include { BCFTOOLS_ROH } from '../../../../modules/bcftools/roh/main.nf'
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workflow test_rhocall_annotate {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
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af_file = [[],[]]
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gen_map = []
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regions = []
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targets = []
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samples = []
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BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
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RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
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}
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workflow test_rhocall_annotate_stub {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
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file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true)]
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af_file = [[],[]]
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gen_map = []
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regions = []
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targets = []
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samples = []
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BCFTOOLS_ROH ( input, af_file, gen_map, regions, samples, targets )
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RHOCALL_ANNOTATE ( input, BCFTOOLS_ROH.out.roh, [])
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}
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