variant-calling/tasks/VEP.wdl

task VEP {

  File vcf
  String sample_id
  String basename = basename(vcf,".vcf")
  String tumor_id
  String normal_id
  File ref_dir
  String fasta
  String vep_path
  File cache
  String hg
  String species
  String vcf2maf_path
  String docker
  String cluster_config
  String disk_size


  command <<<
    set -o pipefail
    set -e
    nt=$(nproc)

    awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${basename}.PASS.vcf
    
    # Define ncbi_build
    if [ ${hg} == "hg19" ]; then
      ncbi_build="GRCh37"
    elif [ ${hg} == "hg38" ]; then
      ncbi_build="GRCh38"
    
    ncol=`awk -F'\t' '{if($1!~"^#"){print NF}}' ${basename}.PASS.vcf | uniq`
    if [ $ncol -lt 11 ]; then
      vcf2maf_ID="--tumor-id ${tumor_id} --normal-id ${normal_id}"
    else
      vcf2maf_ID="--tumor-id ${tumor_id}"
    fi

    nrow=`awk -F'\t' '{if($1~"^chr"){print $0}}' ${basename}.PASS.vcf | wc -l`
    if [ $nrow -lt 5000 ]; then
      buffer_size="--buffer_size 5000"
    else
      buffer_size="--buffer_size 500"
    fi

    # vep
    perl ${vep_path}/vep --format vcf --vcf \
    --assembly $ncbi_build \
    --species ${species} \
    --everything --af_exac \
    --offline \
    --cache --dir_cache ${cache} \
    --fasta ${ref_dir}/${fasta} \
    --input_file ${basename}.PASS.vcf --output_file ${basename}.PASS.vep.vcf


    # vcf2maf
    perl ${vcf2maf_path}/vcf2maf.pl \
    --inhibit-vep \
    --input-vcf ${basename}.PASS.vep.vcf --output-maf ${basename}.PASS.maf \
    $vcf2maf_ID \
    --ref-fasta ${ref_dir}/${fasta} \
    --ncbi-build $ncbi_build \
    --species ${species} \
    --vep-fork $nt
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File input_vcf = "${basename}.PASS.vcf"
    File vep_vcf = "${basename}.PASS.vep.vcf"
    File maf = "${basename}.PASS.maf"
  }
}