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- import "./tasks/gVCF_chromo_split.wdl" as gVCF_chromo_split
- import "./tasks/GVCFtyper.wdl" as GVCFtyper
-
- workflow {{ project_name }} {
-
- File inputSamplesFile
- Array[Array[File]] inputSamples = read_tsv(inputSamplesFile)
-
- String SENTIEON_INSTALL_DIR
- String docker
- String project_name
- String fasta
- File ref_dir
- String disk_size
- String cluster_config
-
- scatter (quartet in inputSamples){
- call gVCF_chromo_split.gVCF_chromo_split as gVCF_chromo_split {
- input:
- gvcf=quartet[0],
- gvcf_idx=quartet[1],
- sample=quartet[2],
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- docker=docker,
- disk_size=disk_size,
- cluster_config=cluster_config
- }
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr1 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr1_gvcf,
- vcf_idx=gVCF_chromo_split.chr1_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr2 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr2_gvcf,
- vcf_idx=gVCF_chromo_split.chr2_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr3 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr3_gvcf,
- vcf_idx=gVCF_chromo_split.chr3_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr4 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr4_gvcf,
- vcf_idx=gVCF_chromo_split.chr4_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr5 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr5_gvcf,
- vcf_idx=gVCF_chromo_split.chr5_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr6 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr6_gvcf,
- vcf_idx=gVCF_chromo_split.chr6_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr7 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr7_gvcf,
- vcf_idx=gVCF_chromo_split.chr7_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr8 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr8_gvcf,
- vcf_idx=gVCF_chromo_split.chr8_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr9 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr9_gvcf,
- vcf_idx=gVCF_chromo_split.chr9_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr10 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr10_gvcf,
- vcf_idx=gVCF_chromo_split.chr10_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr11 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr11_gvcf,
- vcf_idx=gVCF_chromo_split.chr11_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr12 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr12_gvcf,
- vcf_idx=gVCF_chromo_split.chr12_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr13 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr13_gvcf,
- vcf_idx=gVCF_chromo_split.chr13_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr14 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr14_gvcf,
- vcf_idx=gVCF_chromo_split.chr14_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr15 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr15_gvcf,
- vcf_idx=gVCF_chromo_split.chr15_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr16 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr16_gvcf,
- vcf_idx=gVCF_chromo_split.chr16_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr17 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr17_gvcf,
- vcf_idx=gVCF_chromo_split.chr17_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr18 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr18_gvcf,
- vcf_idx=gVCF_chromo_split.chr18_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr19 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr19_gvcf,
- vcf_idx=gVCF_chromo_split.chr19_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr20 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr20_gvcf,
- vcf_idx=gVCF_chromo_split.chr20_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr21 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr21_gvcf,
- vcf_idx=gVCF_chromo_split.chr21_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chr22 {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chr22_gvcf,
- vcf_idx=gVCF_chromo_split.chr22_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- call GVCFtyper.GVCFtyper as GVCFtyper_chrX {
- input:
- ref_dir=ref_dir,
- SENTIEON_INSTALL_DIR=SENTIEON_INSTALL_DIR,
- fasta=fasta,
- vcf=gVCF_chromo_split.chrX_gvcf,
- vcf_idx=gVCF_chromo_split.chrX_gvcf_idx,
- project_name=project_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
- }
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