mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-25 03:58:17 +00:00
fe4eb459fb
* Add stranger * Add when clause * Update paths * Update modules/stranger/main.nf Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se> Co-authored-by: Mahesh Binzer-Panchal <mahesh.binzer-panchal@nbis.se>
19 lines
832 B
Text
19 lines
832 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
|
|
include { STRANGER } from '../../../modules/stranger/main.nf'
|
|
|
|
workflow test_stranger {
|
|
|
|
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 )
|
|
STRANGER ( EXPANSIONHUNTER.out.vcf )
|
|
}
|