mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-23 03:28:17 +00:00
a0bc08732c
* added template for fastqtobam * porting old code into new template * update with missing getprocessname function * test completed - updating all * fixed linting issues * improved reading Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
16 lines
594 B
Text
16 lines
594 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
params.read_structure = "+T 12M11S+T"
|
|
|
|
include { FGBIO_FASTQTOBAM } from '../../../../modules/fgbio/fastqtobam/main.nf' addParams( options: [:] )
|
|
|
|
workflow test_fgbio_fastqtobam {
|
|
|
|
input = [ [ id:'test', single_end:false ], // meta map
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_umi_1_fastq_gz'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_umi_2_fastq_gz'], checkIfExists: true) ]
|
|
]
|
|
|
|
FGBIO_FASTQTOBAM ( input, "${params.read_structure}" )
|
|
}
|