mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-11 12:43:09 +00:00
42 lines
2.3 KiB
Text
42 lines
2.3 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_APPLYVQSR } from '../../../../modules/gatk4/applyvqsr/main.nf'
|
||
|
|
|
||
|
|
workflow test_gatk4_applyvqsr {
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_recal'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_recal_idx'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_tranches'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||
|
|
allelespecific = false
|
||
|
|
truthsensitivity = '99.0'
|
||
|
|
mode = 'SNP'
|
||
|
|
|
||
|
|
GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_applyvqsr_allele_specific {
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_recal_idx'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_allele_specific_tranches'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
|
||
|
|
fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
|
||
|
|
allelespecific = true
|
||
|
|
truthsensitivity = '99.0'
|
||
|
|
mode = 'SNP'
|
||
|
|
|
||
|
|
GATK4_APPLYVQSR ( input, fasta, fai, dict, allelespecific, truthsensitivity, mode )
|
||
|
|
}
|