mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 07:42:05 +00:00
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
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
|
|
|
|
workflow test_expansionhunter {
|
|
|
|
input = [ [ id:'test', gender:'male' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
|
|
]
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
|
variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
|
|
|
|
EXPANSIONHUNTER ( input, fasta, variant_catalog )
|
|
}
|