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;
      (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