Biokepi API : Biokepi_pipeline_edsl.To_workflow.Make.gatk

let gatk_bqsr ?(configuration = Tools.Gatk.Configuration.default_bqsr) bam =
    let input_bam = get_bam (AF.get_file bam) in
    let output_bam =
      let (bqsr, preads) = configuration in
      Name_file.from_path input_bam#product#path
        ~readable_suffix:"gatk_bqsr.bam" [
        bqsr.Tools.Gatk.Configuration.Bqsr.name;
        preads.Tools.Gatk.Configuration.Print_reads.name;
      ] in
    let config_bqsr, config_print_reads = configuration in
    Bam (
      Tools.Gatk.base_quality_score_recalibrator ~configuration
        ~run_with ~input_bam ~output_bam
    )
    |> AF.with_provenance "gatk-bqsr" ["bam", AF.get_provenance bam]
      ~string_arguments:[
        "bqsr-configuration-name",
        config_bqsr.Tools.Gatk.Configuration.Bqsr.name;
        "print-reads-configuration-name",
        config_print_reads.Tools.Gatk.Configuration.Print_reads.name;
      ]
      ~json_arguments:[
        "bqsr-configuration",
        Tools.Gatk.Configuration.Bqsr.to_json config_bqsr;
        "print-reads-configuration",
        Tools.Gatk.Configuration.Print_reads.to_json config_print_reads;
      ]