mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
aed45dd766
* 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>
41 lines
1.8 KiB
Text
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 )
|
|
}
|