mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
409af2f27c
* feat: code polishing * Apply suggestions from code review Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de> * code polishing * more code polishing * code polishing * tests for applybqsrspark * fix typo * no need to check md5sum for versions.yml * fix: use correct syntax * code polishing again * add tests for markduplicatesspark * simplify mergevcfs tests * add tests for baserecalibratorspark * fix: path to entry * code polishing * fix linting * simplify module * update meta.yml * fix pair mode * fix: MITO mode * more tests * fix command * bad copy paste * fix typos * fix tests * fix test * update meta.yml * correct versions.yml in all test.yml * code polishing * code polishing * more code polishing * fix args * add tmpdir for all Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
33 lines
1.3 KiB
Text
33 lines
1.3 KiB
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
|
|
include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
|
|
|
|
workflow test_gatk4_calculatecontamination_tumor_only {
|
|
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
|
|
[] ]
|
|
|
|
GATK4_CALCULATECONTAMINATION ( input )
|
|
}
|
|
|
|
workflow test_gatk4_calculatecontamination_matched_pair {
|
|
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
|
|
|
|
GATK4_CALCULATECONTAMINATION ( input )
|
|
}
|
|
|
|
workflow test_gatk4_calculatecontamination_segmentation {
|
|
|
|
input = [ [ id:'test' ], // meta map
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
|
|
file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
|
|
|
|
GATK4_CALCULATECONTAMINATION_SEGMENTATION ( input )
|
|
}
|