let index
    ~reference_build
    ~(run_with : Machine.t) =
  let open KEDSL in
  let reference_transcriptome =
    Machine.get_reference_genome run_with reference_build
    |> Reference_genome.cdna_exn in
  let kallisto_tool = Machine.get_tool run_with Machine.Tool.Default.kallisto in
  let name =
    sprintf "kallisto-index-%s" (Filename.basename reference_transcriptome#product#path) in
  let reference_dir = (Filename.dirname reference_transcriptome#product#path) in
  let result = sprintf "%s.kallisto.idx" reference_dir in
  workflow_node ~name
    (single_file ~host:(Machine.(as_host run_with)) result)
    ~edges:[
      on_failure_activate (Workflow_utilities.Remove.file ~run_with result);
      depends_on reference_transcriptome;
      depends_on Machine.Tool.(ensure kallisto_tool);
    ]
    ~make:(Machine.run_big_program run_with ~name
             ~self_ids:["kallisto"; "index"]
             Program.(
               Machine.Tool.(init kallisto_tool)
               && shf "kallisto index -i %s %s"
                 result
                 reference_transcriptome#product#path
             ))