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a6cb75174b
* Add optional variant catalog input * fix for no variant catalog test Co-authored-by: ljmesi <37740329+ljmesi@users.noreply.github.com> Co-authored-by: Lauri Mesilaakso <john.mesilaakso@gmail.com>
25 lines
990 B
Text
25 lines
990 B
Text
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
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include { STRANGER } from '../../../modules/stranger/main.nf'
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input = [ [ id:'test', gender:'male' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
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]
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fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
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variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
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workflow test_stranger {
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EXPANSIONHUNTER ( input, fasta, variant_catalog )
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STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
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}
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workflow test_stranger_without_optional_variant_catalog {
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EXPANSIONHUNTER ( input, fasta, variant_catalog )
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STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
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}
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