Biokepi API : Biokepi_pipeline_edsl.To_workflow.Make.bwa_mem

let bwa_mem_opt
      ?(configuration = Tools.Bwa.Configuration.Mem.default)
      ~reference_build
      input =
    let bwa_mem_opt input annot =
      let result_prefix =
        Name_file.in_directory ~readable_suffix:"bwamemopt" Config.work_dir [
          Tools.Bwa.Configuration.Mem.name configuration;
          Tools.Bwa.Input_reads.sample_name input;
          Tools.Bwa.Input_reads.read_group_id input;
        ] in
      Bam (
        Tools.Bwa.mem_align_to_bam
          ~configuration ~reference_build ~run_with ~result_prefix input
      )
      |> AF.with_provenance "bwa-mem-opt" ["input", annot]
        ~string_arguments:[
          "reference-build", reference_build;
          "configuration-name", Tools.Bwa.Configuration.Mem.name configuration;
        ]
        ~json_arguments:[
          "configuration", Tools.Bwa.Configuration.Mem.to_json configuration;
        ]
    in
    let of_input =
      function
      | `Fastq fastq ->
        let fq = get_fastq (AF.get_file fastq) in
        bwa_mem_opt (`Fastq fq) (AF.get_provenance fastq)
      | `Fastq_gz fqz ->
        let fq = get_gz (AF.get_file fqz) |> get_fastq in
        bwa_mem_opt (`Fastq fq) (AF.get_provenance fqz)
      | `Bam (b, p) ->
        let bam = get_bam (AF.get_file b) in
        bwa_mem_opt (`Bam (bam, `PE)) (AF.get_provenance b)
    in
    of_input input