let run ~reference_build     ~(run_with:Machine.t)     ~bam     ~result_prefix =   let open KEDSL in   let name = sprintf "cufflinks-%s" (Filename.basename result_prefix) in   let result_file suffix = result_prefix ^ suffix in   let output_dir = result_file "-cufflinks_output" in   let genes_gtf_output = output_dir // "genes.fpkm_tracking" in   let reference_fasta =     Machine.get_reference_genome run_with reference_build     |> Reference_genome.fasta in   let reference_annotations =     Machine.get_reference_genome run_with reference_build     |> Reference_genome.gtf_exn in   let cufflinks_tool =     Machine.get_tool run_with Machine.Tool.Default.cufflinks in   let sorted_bam =     Samtools.sort_bam_if_necessary ~run_with ~by:`Coordinate bam in   let processors = Machine.max_processors run_with in   let make =     Machine.run_big_program run_with ~name ~processors       ~self_ids:["cufflinks"]       Program.(         Machine.Tool.init cufflinks_tool         && shf "mkdir -p %s" output_dir         && shf "cufflinks -p %d -G %s -o %s %s                 "           processors           reference_annotations#product#path           output_dir           sorted_bam#product#path       )   in   workflow_node ~name ~make     (single_file genes_gtf_output ~host:(Machine.as_host run_with))     ~edges:[       depends_on bam;       depends_on reference_fasta;       depends_on reference_annotations;       depends_on (Machine.Tool.ensure cufflinks_tool);       depends_on (Samtools.index_to_bai ~run_with sorted_bam);     ]