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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
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nextflow.enable.dsl = 2
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include { GATK4_CALCULATECONTAMINATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
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include { GATK4_CALCULATECONTAMINATION as GATK4_CALCULATECONTAMINATION_SEGMENTATION } from '../../../../modules/gatk4/calculatecontamination/main.nf'
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workflow test_gatk4_calculatecontamination_tumor_only {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
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[] ]
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GATK4_CALCULATECONTAMINATION ( input )
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}
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workflow test_gatk4_calculatecontamination_matched_pair {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
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GATK4_CALCULATECONTAMINATION ( input )
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}
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workflow test_gatk4_calculatecontamination_segmentation {
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input = [ [ id:'test' ], // meta map
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file(params.test_data['homo_sapiens']['illumina']['test2_pileups_table'], checkIfExists: true),
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file(params.test_data['homo_sapiens']['illumina']['test_pileups_table'], checkIfExists: true) ]
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GATK4_CALCULATECONTAMINATION_SEGMENTATION ( input )
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}
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