mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
16 lines
743 B
Text
16 lines
743 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_MERGEBAMALIGNMENT } from '../../../../modules/gatk4/mergebamalignment/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_gatk4_mergebamalignment {
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
|
|
]
|
|
unmapped = 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, unmapped, fasta, dict )
|
|
}
|