nf-core_modules/tests/software/strelka/germline/main.nf

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#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { STRELKA_GERMLINE } from '../../../../software/strelka/germline/main.nf' addParams( options: [:] )
workflow test_strelka_germline {
input = [
[ id:'test'], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], 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)
targets = []
STRELKA_GERMLINE ( input, fasta, fai, targets )
}
workflow test_strelka_germline_target_bed {
input = [
[ id:'test'], // meta map
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], 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)
targets = file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
STRELKA_GERMLINE ( input, fasta, fai, targets )
}