variant-calling/tasks/annovar.wdl

task annovar {

  String sample
  File vcf
  String annotated_vcf = basename(vcf,".vcf")
  String hg
  File database
  String docker
  String cluster_config
  String disk_size


  command <<<
    set -o pipefail
    set -e
    nt=$(nproc)
    /installations/annovar/table_annovar.pl ${vcf} ${database} -buildver ${hg} -hgvs -out ${annotated_vcf} -remove -protocol refGene,cytoBand,genomicSuperDups,ljb26_all,dbnsfp35c,intervar_20180118,cosmic70,exac03,gnomad211_exome,clinvar_20200316 -operation g,r,r,f,f,f,f,f,f,f -nastring . -vcfinput -thread $nt
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File avinput = "${annotated_vcf}.avinput"
    File multianno_txt = "${annotated_vcf}.multianno.txt"
    File multianno = "${annotated_vcf}.multianno.vcf"
  }
}