Biokepi API : Biokepi_pipeline_edsl.To

let snpeff vcf =
    let open KEDSL in
    let v = get_vcf (AF.get_file vcf) in
    let reference_build = v#product#reference_build in
    let out_folder =
      Name_file.in_directory ~readable_suffix:"snpeff" Config.work_dir
        [ Filename.basename v#product#path; reference_build; ]
    in
    let snpeff_run =
      Tools.Snpeff.annotate ~run_with ~reference_build ~input_vcf:v ~out_folder
    in
    Vcf (
      workflow_node
        (transform_vcf v#product ~path:(snpeff_run#product#path))
        ~name:(sprintf "Fetch annotated VCF: %s" v#render#name) 
        ~edges:[ depends_on snpeff_run; ]
    )
    |> AF.with_provenance "snpeff" ["vcf", AF.get_provenance vcf]