let mem_align_to_sam     ~reference_build     ?(configuration = Configuration.Mem.default)     ~fastq     (* ~(r1: KEDSL.single_file KEDSL.workflow_node) *)     (* ?(r2: KEDSL.single_file KEDSL.workflow_node option) *)     ~(result_prefix:string)     ~(run_with : Machine.t)     () =   let open KEDSL in   let reference_fasta =     Machine.get_reference_genome run_with reference_build     |> Reference_genome.fasta in   let in_work_dir =     Program.shf "cd %s" Filename.(quote (dirname result_prefix)) 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 bwa_index = index ~reference_build ~run_with in   let result = sprintf "%s.sam" result_prefix in   let r1_path, r2_path_opt = fastq#product#paths in   let name = sprintf "bwa-mem-%s" (Filename.basename r1_path) in   let processors = Machine.max_processors run_with in   let bwa_base_command =     String.concat ~sep:" " [       "bwa mem";       (read_group_header_option `Mem          ~sample_name:fastq#product#escaped_sample_name          ~read_group_id:(Filename.basename r1_path));       "-t"; Int.to_string processors;       "-O"; Int.to_string configuration.Configuration.Mem.gap_open_penalty;       "-E"; Int.to_string configuration.Configuration.Mem.gap_extension_penalty;       "-B"; Int.to_string configuration.Configuration.Mem.mismatch_penalty;       (Filename.quote reference_fasta#product#path);       (Filename.quote r1_path);     ] in   let bwa_base_target ~bwa_command  =     workflow_node       (single_file result ~host:Machine.(as_host run_with))       ~name       ~edges:(         depends_on Machine.Tool.(ensure bwa_tool)         :: depends_on bwa_index         :: depends_on fastq         :: on_failure_activate (Remove.file ~run_with result)         :: [])       ~tags:[Target_tags.aligner]       ~make:(Machine.run_big_program run_with ~processors ~name                ~self_ids:["bwa"; "mem"]                Program.(                  Machine.Tool.(init bwa_tool)                  && in_work_dir                  && sh bwa_command))   in   match r2_path_opt with   | Some read2 ->     let bwa_command =       String.concat ~sep:" " [         bwa_base_command;         (Filename.quote read2);         ">"; (Filename.quote result);       ] in     bwa_base_target ~bwa_command   | None ->     let bwa_command =       String.concat ~sep:" " [         bwa_base_command;         ">"; (Filename.quote result);       ] in     bwa_base_target ~bwa_command