Example WDL

example.wdl

task M2 {
  File ref_fasta
  File ref_fasta_dict
  File ref_fasta_fai
  File tumor_bam
  File tumor_bai
  File normal_bam
  File normal_bai
  File intervals
  String m2_output_vcf_name
  
  command {
    java -jar /task/GenomeAnalysisTK_latest_unstable.jar -T M2 \
    --no_cmdline_in_header -dt NONE -ip 50 \
    -R ${ref_fasta} \
    -I:tumor ${tumor_bam} \
    -I:normal ${normal_bam} \
    -L ${intervals} \
    -o ${m2_output_vcf_name} \
    --disable_auto_index_creation_and_locking_when_reading_rods
  }
  runtime {
    docker: "gcr.io/broad-dsde-dev/cep3"
  }
  output {
    File m2_output_vcf = "${m2_output_vcf_name}"
  }
}

workflow CancerExomePipeline_v2 {
  call M2
}