let run ~(run_with: Machine.t) ~reference_build ~vcf ~output_vcf =   let open KEDSL in   let vap_tool =     Machine.get_tool run_with       Machine.Tool.Definition.(create "vcf-annotate-polyphen"in   let whessdb = Machine.(get_reference_genome run_with reference_build)     |> Reference_genome.whess_exn   in   let whessdb_path = whessdb#product#path in   let vcf_path = vcf#product#path in   let name = sprintf "vcf-annotate-polyphen_%s" (Filename.basename vcf_path) in   workflow_node     (transform_vcf vcf#product ~path:output_vcf)     ~name     ~edges:[       depends_on Machine.Tool.(ensure vap_tool);       depends_on whessdb;       depends_on vcf;     ]     ~make:(       Machine.run_program run_with ~name         Program.(           Machine.Tool.(init vap_tool)           && shf "vcf-annotate-polyphen %s %s %s" whessdb_path vcf_path output_vcf         )     )