Biokepi API : Biokepi_pipeline_edsl.To

let delly2 ?(configuration=Tools.Delly2.Configuration.default)
      ~normal ~tumor () =
    let normal_bam = get_bam (AF.get_file normal) in
    let tumor_bam = get_bam (AF.get_file tumor) in
    let output_path =
      Name_file.in_directory ~readable_suffix:"-delly2.vcf" Config.work_dir [
        normal_bam#product#path;
        tumor_bam#product#path;
        Tools.Delly2.Configuration.name configuration;
      ]
    in
    let bcf =
      Tools.Delly2.run_somatic
        ~configuration
        ~run_with
        ~normal:normal_bam ~tumor:tumor_bam
        ~output_path:(output_path ^ ".bcf")
    in
    Vcf (Tools.Bcftools.bcf_to_vcf ~run_with
           ~reference_build:normal_bam#product#reference_build
           ~bcf output_path)
    |> AF.with_provenance "delly2"
      ["normal", AF.get_provenance normal; "tumor", AF.get_provenance tumor]
      ~string_arguments:[
        "configuration-name", Tools.Delly2.Configuration.name configuration;
      ]
      ~json_arguments:[
        "configuration", Tools.Delly2.Configuration.to_json configuration;
      ]