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

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { EXPANSIONHUNTER } from '../../../modules/expansionhunter/main.nf'
include { STRANGER } from '../../../modules/stranger/main.nf'
input = [ [ id:'test', gender:'male' ], // meta map
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true),
]
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
variant_catalog = file(params.test_data['homo_sapiens']['genome']['repeat_expansions'], checkIfExists: true)
workflow test_stranger {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, variant_catalog )
}
workflow test_stranger_without_optional_variant_catalog {
EXPANSIONHUNTER ( input, fasta, variant_catalog )
STRANGER ( EXPANSIONHUNTER.out.vcf, [] )
}