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19 lines
789 B
Text
Executable file
19 lines
789 B
Text
Executable file
#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { CNVKIT } from '../../../software/cnvkit/main.nf' addParams( options: [ 'args': '--output-reference reference.cnn' ] )
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workflow test_cnvkit {
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tumourbam = file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true)
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normalbam = file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true)
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input = [ [ id:'test' ], // meta map
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tumourbam,
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normalbam
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]
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fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
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targets = file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
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CNVKIT ( input, fasta, targets )
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}
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