mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 19:18:17 +00:00
7d0ddbc8ab
* Add atlas/call * Apply suggestions from code review * Update modules/atlas/call/main.nf Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com> * Apply suggestions from code review Co-authored-by: Thiseas C. Lamnidis <thisseass@gmail.com>
22 lines
823 B
Text
22 lines
823 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { ATLAS_CALL } from '../../../../modules/atlas/call/main.nf'
|
|
|
|
workflow test_atlas_call {
|
|
|
|
input = [
|
|
[ id:'test', single_end:false ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
|
recal = []
|
|
pmd = []
|
|
known_alleles = []
|
|
method = 'randomBase'
|
|
|
|
ATLAS_CALL ( input, fasta, fai, recal, pmd, known_alleles, method )
|
|
}
|