nf-core_modules/tests/modules/gatk4/variantfiltration/main.nf
Harshil Patel e937c7950a
Rename software/ directory to modules/ to re-organise module structure (#567)
* 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
2021-07-07 10:10:18 +01:00

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
test_options = ['args': '--filter-name "test_filter" --filter-expression "MQ0 > 0"', 'suffix': '.filtered']
include { GATK4_VARIANTFILTRATION } from '../../../../modules/gatk4/variantfiltration/main.nf' addParams( options: test_options )
workflow test_gatk4_variantfiltration {
input = [ [ id:'test' ], // meta map
[ file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true) ]
]
fasta = [ file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true) ]
fai = [ file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true) ]
genome_dict = [ file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true) ]
GATK4_VARIANTFILTRATION ( input, fasta, fai, genome_dict )
}