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              ))