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49b18b1639
* add stub section * add stub for bcftools norm * add stub to more modules * fix expansionhunter tests * revert changes -picard * Update stub to write version no.s to a file * add picard * revert picard again * add stubs to more modules * fix bwamem2 * add bcftools view * add stubs * fix svdb query * review suggestions
17 lines
736 B
Text
17 lines
736 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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workflow test_expansionhunter {
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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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EXPANSIONHUNTER ( input, fasta, variant_catalog )
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}
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