mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-11-13 05:13:09 +00:00
63 lines
4.1 KiB
Text
63 lines
4.1 KiB
Text
|
#!/usr/bin/env nextflow
|
||
|
|
|
||
|
|
nextflow.enable.dsl = 2
|
||
|
|
|
||
|
|
include { GATK4_MUTECT2 } from '../../../../modules/gatk4/mutect2/main.nf' addParams( options: [:] )
|
||
|
|
|
||
|
|
workflow test_gatk4_mutect2_tumor_normal_pair {
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true) , file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||
|
|
["testN"]
|
||
|
|
]
|
||
|
|
run_single = false
|
||
|
|
run_pon = false
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
|
||
|
|
germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
|
||
|
|
panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_mutect2_tumor_single {
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
run_single = true
|
||
|
|
run_pon = false
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
germline_resource = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz'], checkIfExists: true)
|
||
|
|
germline_resource_idx = file(params.test_data['homo_sapiens']['genome']['gnomad_r2_1_1_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
panel_of_normals = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz'], checkIfExists: true)
|
||
|
|
panel_of_normals_idx = file(params.test_data['homo_sapiens']['genome']['mills_and_1000g_indels_vcf_gz_tbi'], checkIfExists: true)
|
||
|
|
|
||
|
|
GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
|
||
|
|
}
|
||
|
|
|
||
|
|
workflow test_gatk4_mutect2_generate_pon {
|
||
|
|
input = [ [ id:'test'], // meta map
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam'], checkIfExists: true)],
|
||
|
|
[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_bam_bai'], checkIfExists: true)],
|
||
|
|
[]
|
||
|
|
]
|
||
|
|
run_single = false
|
||
|
|
run_pon = true
|
||
|
|
fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
|
||
|
|
fastaidx = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
|
||
|
|
dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
|
||
|
|
germline_resource = []
|
||
|
|
germline_resource_idx = []
|
||
|
|
panel_of_normals = []
|
||
|
|
panel_of_normals_idx = []
|
||
|
|
|
||
|
|
GATK4_MUTECT2 ( input , run_single , run_pon , fasta , fastaidx , dict , germline_resource, germline_resource_idx , panel_of_normals , panel_of_normals_idx )
|
||
|
|
}
|