VEP/workflow.wdl

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
  String vep_path
  File cache
  String ncbi_build
  String species
  String vep_docker
  String cluster_config
  String disk_size

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