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- import "./tasks/in_out.wdl" as in_out
- import "./tasks/region.wdl" as region
-
-
- workflow {{ project_name }} {
-
- File vcf
- File vcf_idx
-
- File confidence_bed
-
- File satellite
- File simple_repeat
- File SINE
- File LINE
- File LTR
- File low_complexity
- File SD
- File ins_breakpoint
- File del_breakpoint
- File mhc
-
- String sample_name
-
- String docker
- String cluster_config
- String disk_size
-
- call in_out.in_out as in_out {
- input:
- vcf=vcf,
- vcf_idx=vcf_idx,
- confidence_bed=confidence_bed,
- sample_name=sample_name,
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
-
- call region.region as region {
- input:
- sub_vcf=in_out.in_vcf,
- sub_vcf_idx=in_out.in_vcf_idx,
- satellite=satellite,
- simple_repeat=simple_repeat,
- SINE=SINE,
- LINE=LINE,
- LTR=LTR,
- low_complexity=low_complexity,
- SD=SD,
- ins_breakpoint=ins_breakpoint,
- del_breakpoint=del_breakpoint,
- mhc=mhc,
- sample_name=sample_name,
- tag="inside",
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
-
- call region.region as region {
- input:
- sub_vcf=in_out.out_vcf,
- sub_vcf_idx=in_out.out_vcf_idx,
- satellite=satellite,
- simple_repeat=simple_repeat,
- SINE=SINE,
- LINE=LINE,
- LTR=LTR,
- low_complexity=low_complexity,
- SD=SD,
- ins_breakpoint=ins_breakpoint,
- del_breakpoint=del_breakpoint,
- mhc=mhc,
- sample_name=sample_name,
- tag="outside",
- docker=docker,
- cluster_config=cluster_config,
- disk_size=disk_size
- }
-
- }
-
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