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
  Boolean only_pass
  String vcf2maf_path
  String docker
  String cluster_config
  String disk_size


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

    if [ only_pass ]; then
      awk -F'\t' '{if(($1~"^#")||($1!~"^#" && $7=="PASS")){print $0}}' ${vcf} > ${sample_id}.INPUT.vcf
    else
      cp ${vcf} ${sample_id}.INPUT.vcf
    fi

    # Define ncbi_build
    if [ hg == "hg19" ]; then
      ncbi_build="GRCh37"
    elif [ hg == "hg38" ]; then
      ncbi_build="GRCh38"
    fi

    # Extract the BND variants from VCF
    awk -F'\t' '{if(($1~"^#")||($8!~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.vcf2maf.vcf
    awk -F'\t' '{if(($1~"^#")||($8~".*SVTYPE=BND.*")){print $0}}' ${sample_id}.INPUT.vcf > ${sample_id}.INPUT.VEP.vcf

    # vcf2maf
    perl ${vcf2maf_path}/vcf2maf.pl \
    --input-vcf ${sample_id}.INPUT.vcf2maf.vcf --output-maf ${basename}.maf \
    --tumor-id ${tumor_id} --normal-id ${normal_id} \
    --ref-fasta ${ref_dir}/${fasta} \
    --vep-path ${vep_path} \
    --vep-data ${cache} \
    --ncbi-build $ncbi_build \
    --species ${species} \
    --vep-fork $nt

    # vep: only annotate the BND
    perl ${vep_path}/vep \
    --input_file ${sample_id}.INPUT.VEP.vcf --output_file ${basename}.BND.VEP.txt \
    --fasta ${ref_dir}/${fasta} \
    --dir ${cache} \
    --assembly $ncbi_build \
    --species ${species} \
    --fork $nt \
    --no_progress --no_stats --buffer_size 5000 --sift b --ccds --uniprot --hgvs --symbol --numbers --domains --gene_phenotype --canonical --protein --biotype --uniprot --tsl --variant_class --shift_hgvs 1 --check_existing --total_length --allele_number --no_escape --xref_refseq --failed 1 --tab --flag_pick_allele --pick_order canonical,tsl,biotype,rank,ccds,length --format vcf --force_overwrite --offline --pubmed --regulatory
  >>>
  
  runtime {
    docker: docker
    cluster: cluster_config
    systemDisk: "cloud_ssd 40"
    dataDisk: "cloud_ssd " + disk_size + " /cromwell_root/"
  }

  output {
    File input_vcf = "${sample_id}.INPUT.vcf"
    File maf = "${basename}.${hg}.maf"
    File bnd_vep = "${basename}.BND.VEP.txt"
  }
}