nf-core_modules/tests/modules/multivcfanalyzer/main.nf
James A. Fellows Yates aed45dd766
Add MultiVCFAnalyzer (#1845)
* Add MultiVCFAnalyzer

* Fix versions

* Fix tests due to md5sum var

* Apply suggestions from code review

* Linting

* Apply suggestions from code review

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>

Co-authored-by: Robert A. Petit III <robbie.petit@gmail.com>
2022-07-05 09:47:10 +02:00

41 lines
1.8 KiB
Text

#!/usr/bin/env nextflow
nextflow.enable.dsl = 2
include { GATK_UNIFIEDGENOTYPER } from '../../../modules/gatk/unifiedgenotyper/main.nf'
include { GUNZIP } from '../../../modules/gunzip/main.nf'
include { MULTIVCFANALYZER } from '../../../modules/multivcfanalyzer/main.nf'
workflow test_multivcfanalyzer {
input = Channel.of([ [ 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),
],
[ [ id:'test2' ], // meta map
file(params.test_data['sarscov2']['illumina']['test_single_end_sorted_bam'], checkIfExists: true),
file(params.test_data['sarscov2']['illumina']['test_single_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)
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
GATK_UNIFIEDGENOTYPER ( input, fasta, fai, dict, [], [], [], [])
mva_vcf = GUNZIP ( GATK_UNIFIEDGENOTYPER.out.vcf ).gunzip
.map{it[1]}
.collect()
.dump()
snpeff_results = []
gff = []
allele_freqs = true
genotype_quality = 30
coverage = 5
homozygous_freq = 0.8
heterozygous_freq = 0.2
gff_exclude = []
MULTIVCFANALYZER ( mva_vcf, fasta, snpeff_results, gff, allele_freqs, genotype_quality, coverage, homozygous_freq, heterozygous_freq, gff_exclude )
}