mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-27 15:53:16 -05:00
55 lines
2.5 KiB
Text
55 lines
2.5 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_REBLOCKGVCF } from '../../../../modules/gatk4/reblockgvcf/main.nf'
|
||
|
|
|
||
|
|
workflow test_gatk4_reblockgvcf {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_reblockgvcf_intervals {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['illumina']['test_vcf_gz_tbi'], checkIfExists: true),
|
||
|
|
file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fasta_index = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, [], [] )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_reblockgvcf_dbsnp {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_haplotc_cnn_vcf_gz_tbi'], checkIfExists: true),
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fasta_index = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz'], checkIfExists: true)
|
||
|
|
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_146_hg38_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_REBLOCKGVCF ( input, fasta, fasta_index, dict, dbsnp, dbsnp_tbi )
|
||
|
|
}
|