mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-24 11:48:17 +00:00
38 lines
1.5 KiB
Text
38 lines
1.5 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { CONTROLFREEC } from '../../../modules/controlfreec/main.nf'
|
||
|
|
include { UNTAR } from '../../../modules/untar/main.nf'
|
||
|
|
workflow test_controlfreec {
|
||
|
|
|
||
|
|
input = [
|
||
|
|
[ id:'test', single_end:false, sex:'XX' ], // meta map
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test_mpileup'], checkIfExists: true),
|
||
|
|
file(params.test_data['homo_sapiens']['illumina']['test2_mpileup'], 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)
|
||
|
|
|
||
|
|
dbsnp = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
|
||
|
|
dbsnp_tbi = file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
|
||
|
|
chrfiles = file(params.test_data['homo_sapiens']['genome']['genome_21_chromosomes_dir'], checkIfExists: true)
|
||
|
|
target_bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
|
||
|
|
|
||
|
|
UNTAR(chrfiles)
|
||
|
|
CONTROLFREEC ( input,
|
||
|
|
fasta,
|
||
|
|
fai,
|
||
|
|
[],
|
||
|
|
dbsnp,
|
||
|
|
dbsnp_tbi,
|
||
|
|
UNTAR.out.untar,
|
||
|
|
[],
|
||
|
|
target_bed,
|
||
|
|
[]
|
||
|
|
)
|
||
|
|
}
|