digraph RNAseq {
  #rankdir=LR;
  compound=true;

  # Links
  CALL_StarAlign -> CALL_MergeBamAlignment
  CALL_BaseRecalibrator -> CALL_ApplyBQSR
  CALL_MarkDuplicates -> CALL_SplitNCigarReads
  CALL_RevertSam -> CALL_SamToFastq
  CALL_SplitNCigarReads -> CALL_BaseRecalibrator
  SCATTER_1_VARIABLE_interval -> CALL_HaplotypeCaller
  CALL_HaplotypeCaller -> CALL_MergeVCFs
  CALL_StarGenerateReferences -> CALL_StarAlign
  CALL_MergeBamAlignment -> CALL_MarkDuplicates
  CALL_gtfToCallingIntervals -> CALL_ScatterIntervalList
  CALL_MergeVCFs -> CALL_VariantFiltration
  CALL_ScatterIntervalList -> SCATTER_1_VARIABLE_interval
  CALL_SplitNCigarReads -> CALL_ApplyBQSR
  CALL_ApplyBQSR -> CALL_HaplotypeCaller
  CALL_RevertSam -> CALL_MergeBamAlignment
  CALL_SamToFastq -> CALL_StarAlign

  # Nodes
  CALL_MergeBamAlignment [label="call MergeBamAlignment"]
  CALL_ApplyBQSR [label="call ApplyBQSR"]
  CALL_gtfToCallingIntervals [label="call gtfToCallingIntervals"]
  subgraph cluster_0 {
    style="filled,dashed";
    fillcolor=white;
    CALL_StarGenerateReferences [label="call StarGenerateReferences"]
    CONDITIONAL_0_EXPRESSION [shape="hexagon" label="if (!(defined(zippedStarReferences)))" style="dashed" ]
  }
  CALL_VariantFiltration [label="call VariantFiltration"]
  CALL_SamToFastq [label="call SamToFastq"]
  CALL_MarkDuplicates [label="call MarkDuplicates"]
  CALL_ScatterIntervalList [label="call ScatterIntervalList"]
  subgraph cluster_1 {
    style="filled,solid";
    fillcolor=white;
    CALL_HaplotypeCaller [label="call HaplotypeCaller"]
    SCATTER_1_VARIABLE_interval [shape="hexagon" label="scatter over File as interval"]
  }
  CALL_MergeVCFs [label="call MergeVCFs"]
  CALL_BaseRecalibrator [label="call BaseRecalibrator"]
  CALL_RevertSam [label="call RevertSam"]
  CALL_SplitNCigarReads [label="call SplitNCigarReads"]
  CALL_StarAlign [label="call StarAlign"]
}