mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 04:33:10 +00:00
e937c7950a
* Update README * Rename pytest_software.yml to pytest_modules.yml * Rename main software directory to modules * Remove deprecated modules * Rename tests software to modules * Replace paths for tests in pytest_modules.yml * Replace software with modules in Github Actions * Replace software with modules in main.nf tests * Rename software to modules in test.yml
29 lines
814 B
Text
29 lines
814 B
Text
#!/usr/bin/env nextflow
|
|
|
|
nextflow.enable.dsl = 2
|
|
|
|
include { BEDTOOLS_GENOMECOV } from '../../../../modules/bedtools/genomecov/main.nf' addParams( options: [suffix: '_out'] )
|
|
|
|
workflow test_bedtools_genomecov {
|
|
input = [
|
|
[ id:'test'],
|
|
file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
|
|
]
|
|
|
|
sizes = file('dummy_chromosome_sizes')
|
|
extension = 'txt'
|
|
|
|
BEDTOOLS_GENOMECOV ( input, sizes, extension )
|
|
}
|
|
|
|
workflow test_bedtools_genomecov_nonbam {
|
|
input = [
|
|
[ id:'test'],
|
|
file(params.test_data['sarscov2']['genome']['baits_bed'], checkIfExists: true)
|
|
]
|
|
|
|
sizes = file(params.test_data['sarscov2']['genome']['genome_sizes'], checkIfExists: true)
|
|
extension = 'txt'
|
|
|
|
BEDTOOLS_GENOMECOV ( input, sizes, extension )
|
|
}
|