Biokepi API : Biokepi_pipeline_edsl.To

let seq2hla fq =
    let fastq = get_fastq (AF.get_file fq) in
    let r1 = KEDSL.read_1_file_node fastq in
    let r2 =
      match KEDSL.read_2_file_node fastq with
      | Some r -> r
      | None ->
        failf "Seq2HLA doesn't support Single_end_sample(s)."
    in
    let work_dir =
      Name_file.in_directory Config.work_dir
        ~readable_suffix:"seq2hla-workdir" [
        fastq#product#escaped_sample_name;
        fastq#product#fragment_id_forced;
      ]
    in
    Seq2hla_result (
      Tools.Seq2HLA.hla_type
        ~work_dir ~run_with ~run_name:fastq#product#escaped_sample_name ~r1 ~r2
    )
    |> AF.with_provenance "seq2hla" ["fastq", AF.get_provenance fq]