mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-09-21 15:52:05 +00:00
27 lines
1.3 KiB
Text
27 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf'
|
|
|
|
workflow test_gatk4_mergebamalignment {
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
|
|
|
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
|
|
}
|
|
|
|
workflow test_gatk4_mergebamalignment_stubs {
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true),
|
|
file(params.test_data['sarscov2']['illumina']['test_unaligned_bam'], checkIfExists: true)
|
|
]
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
|
|
|
GATK4_MERGEBAMALIGNMENT ( input, fasta, dict )
|
|
}
|