let index
    ~reference_build
    ~(run_with : Machine.t) =
  let open KEDSL in
  let reference_fasta =
    Machine.get_reference_genome run_with reference_build
    |> Reference_genome.fasta in
  let star_tool = Machine.get_tool run_with Machine.Tool.Default.star in
  let name =
    sprintf "star-index-%s" (Filename.basename reference_fasta#product#path) in
  let reference_annotations =
    Machine.get_reference_genome run_with reference_build |> Reference_genome.gtf_exn in
  let reference_dir = (Filename.dirname reference_fasta#product#path) in
  let result_dir = sprintf "%s/star-index/" reference_dir in
  let suffix_array_result = result_dir // "SA" in
  let processors = Machine.max_processors run_with in
  workflow_node ~name
    (single_file ~host:(Machine.(as_host run_with)) suffix_array_result)
    ~edges:[
      on_failure_activate (Remove.directory ~run_with result_dir);
      depends_on reference_fasta;
      depends_on Machine.Tool.(ensure star_tool);
    ]
    ~tags:[Target_tags.aligner]
    ~make:(Machine.run_big_program run_with ~processors ~name
             ~self_ids:["star"; "index"]
             Program.(
               Machine.Tool.(init star_tool)
               && shf "mkdir %s" result_dir
               && shf "STAR --runMode genomeGenerate --genomeDir %s --genomeFastaFiles %s --sjdbGTFfile %s --runThreadN %d"
                 result_dir
                 (Filename.quote reference_fasta#product#path)
                 (Filename.quote reference_annotations#product#path)
                 processors
             ))