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aa32a8a72e
* initiated files for calculate contamination * pushing local repo to remote * created script, filled in meta yml, created tests and test yml. local checks passing, needs repo side test data * added option and tests for outputting optional segmentation file * saving for test push * versions updated, test data added * Update main.nf * fixed versions info, should report correctly now * small update to main.nf outputs formatting * Apply suggestions from code review * Update test_data.config * Apply suggestions from code review Co-authored-by: GCJMackenzie <gavin.mackenzie@nibsc.org> Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
38 lines
1.3 KiB
Text
38 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' addParams( options: [:] )
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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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segmentout = false
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GATK4_CALCULATECONTAMINATION ( input, segmentout )
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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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segmentout = false
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GATK4_CALCULATECONTAMINATION ( input, segmentout )
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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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segmentout = true
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GATK4_CALCULATECONTAMINATION ( input, segmentout )
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}
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