|
|
@@ -1,13 +1,13 @@ |
|
|
|
import "./tasks/vcf2maf.wdl" as vcf2maf |
|
|
|
|
|
|
|
workflow {{ project_name }} { |
|
|
|
|
|
|
|
|
|
|
|
File vcf |
|
|
|
String sample_id |
|
|
|
String tumor_id |
|
|
|
String normal_id |
|
|
|
File ref_dir |
|
|
|
String fasta |
|
|
|
File ref_dir |
|
|
|
String fasta |
|
|
|
String vep_path |
|
|
|
File cache |
|
|
|
String ncbi_build |
|
|
@@ -16,9 +16,9 @@ workflow {{ project_name }} { |
|
|
|
String cluster_config |
|
|
|
String disk_size |
|
|
|
|
|
|
|
call vcf2maf.vcf2maf as vcf2maf { |
|
|
|
input: |
|
|
|
vcf=vcf, |
|
|
|
call vcf2maf.vcf2maf as vcf2maf { |
|
|
|
input: |
|
|
|
vcf=vcf, |
|
|
|
tumor_id=tumor_id, |
|
|
|
normal_id=normal_id, |
|
|
|
ref_dir=ref_dir, |
|
|
@@ -27,8 +27,8 @@ workflow {{ project_name }} { |
|
|
|
cache=cache, |
|
|
|
ncbi_build=ncbi_build, |
|
|
|
species=species, |
|
|
|
docker=vep_docker, |
|
|
|
cluster_config=cluster_config, |
|
|
|
disk_size=disk_size |
|
|
|
} |
|
|
|
docker=vep_docker, |
|
|
|
cluster_config=cluster_config, |
|
|
|
disk_size=disk_size |
|
|
|
} |
|
|
|
} |