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
  (* `bwa index` creates a bunch of files, c.f.
     [this question](https://www.biostars.org/p/73585/) we detect the
     `.bwt` one. *)
  let bwa_tool = Machine.get_tool run_with Machine.Tool.Default.bwa in
  let name =
    sprintf "bwa-index-%s" (Filename.basename reference_fasta#product#path) in
  let result = sprintf "%s.bwt" reference_fasta#product#path in
  workflow_node ~name
    (single_file ~host:(Machine.(as_host run_with)) result)
    ~edges:[
      on_failure_activate (Remove.file ~run_with result);
      depends_on reference_fasta;
      depends_on Machine.Tool.(ensure bwa_tool);
    ]
    ~tags:[Target_tags.aligner]
    ~make:(Machine.run_big_program run_with ~name
             ~self_ids:["bwa"; "index"]
             Program.(
               Machine.Tool.(init bwa_tool)
               && shf "bwa index %s"
                 (Filename.quote reference_fasta#product#path)))