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

  # Links
  CALL_alignment -> CALL_msi
  CALL_alignment -> CALL_mutation_calling
  CALL_tumor_content -> CALL_cnvkit
  CALL_alignment -> CALL_fusion
  CALL_alignment -> CALL_cnvkit
  CALL_qc -> CALL_alignment
  CALL_mutation_calling -> CALL_annovar
  CALL_alignment -> CALL_chemo
  CALL_mutation_calling -> CALL_neoantigen
  CALL_alignment -> CALL_tumor_content
  CALL_hla -> CALL_neoantigen
  CALL_alignment -> CALL_annovar
  CALL_annovar -> CALL_tmb

  # Nodes
  CALL_alignment [label="call alignment";shape="oval";peripheries=2]
  CALL_tumor_content [label="call tumor_content"]
  CALL_mutation_calling [label="call mutation_calling"]
  CALL_annovar [label="call annovar"]
  CALL_cnvkit [label="call cnvkit"]
  CALL_msi [label="call msi"]
  CALL_fusion [label="call fusion"]
  CALL_neoantigen [label="call neoantigen"]
  CALL_tmb [label="call tmb"]
  CALL_create_dir [label="call create_dir"]
  CALL_hla [label="call hla"]
  CALL_qc [label="call qc";shape="oval";peripheries=2]
  CALL_chemo [label="call chemo"]
}