let cufflinks ?reference_build bamf =     let bam = get_bam (AF.get_file bamf) in     let reference_build =       match reference_build with       | None -> bam#product#reference_build       | Some r -> r in     let result_prefix =       Name_file.in_directory ~readable_suffix:"cufflinks" Config.work_dir [         bam#product#escaped_sample_name;         reference_build       ] in     Cufflinks_result (       Tools.Cufflinks.run         ~reference_build ~bam ~run_with ~result_prefix     )     |> AF.with_provenance "cufflinks" ["bam", AF.get_provenance bamf]       ~string_arguments:["reference-build", reference_build]