nf-core_modules/tests/modules/cnvkit/main.nf

20 lines
769 B
Text
Raw Normal View History

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