seqhla-biokepi.ml

let seq2hla_from_bam
    ~path
    ~sample =
  let open Biokepi.KEDSL in
  let open Biokepi.Pipeline.Construct in
  let reference_build = "b37" in
  let work_dir =
    Biokepi.Machine.work_dir Demeter.machine
    // "mskcc-bladder-rna" in
  let initial_bam =
    workflow_node
      (bam_file ~host:Demeter.host ~reference_build path)
  in
  let pipeline = 
    Biokepi.Pipeline.Construct.(
          bam ~dataset:sample initial_bam
          |> bam_to_fastq `Paired
          |> seq2hla
        )
  in
  let hla_results =
    let compiler =
      Compiler.create ()
        ~processors:8
        ~reference_build
        ~work_dir
        ~machine: Demeter.machine
    in
    Compiler.seq2hla_hla_types_step ~compiler pipeline  
  in
  hla_results