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master
YaqingLiu 4 years ago
parent
commit
0c0dfc94bc
2 changed files with 12 additions and 12 deletions
  1. +2
    -2
      tasks/vcf2maf.wdl
  2. +10
    -10
      workflow.wdl

+ 2
- 2
tasks/vcf2maf.wdl View File

String basename = basename(vcf,".vcf") String basename = basename(vcf,".vcf")
String tumor_id String tumor_id
String normal_id String normal_id
File ref_dir
String fasta
File ref_dir
String fasta
String vep_path String vep_path
File cache File cache
String ncbi_build String ncbi_build

+ 10
- 10
workflow.wdl View File

import "./tasks/vcf2maf.wdl" as vcf2maf import "./tasks/vcf2maf.wdl" as vcf2maf


workflow {{ project_name }} { workflow {{ project_name }} {
File vcf File vcf
String sample_id String sample_id
String tumor_id String tumor_id
String normal_id String normal_id
File ref_dir
String fasta
File ref_dir
String fasta
String vep_path String vep_path
File cache File cache
String ncbi_build String ncbi_build
String cluster_config String cluster_config
String disk_size String disk_size


call vcf2maf.vcf2maf as vcf2maf {
input:
vcf=vcf,
call vcf2maf.vcf2maf as vcf2maf {
input:
vcf=vcf,
tumor_id=tumor_id, tumor_id=tumor_id,
normal_id=normal_id, normal_id=normal_id,
ref_dir=ref_dir, ref_dir=ref_dir,
cache=cache, cache=cache,
ncbi_build=ncbi_build, ncbi_build=ncbi_build,
species=species, species=species,
docker=vep_docker,
cluster_config=cluster_config,
disk_size=disk_size
}
docker=vep_docker,
cluster_config=cluster_config,
disk_size=disk_size
}
} }

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