struct open Biokepi_run_environment open Common module Remove = Workflow_utilities.Remove let bam_left_align ~(run_with : Machine.t) ~reference_build ~bam output_file_path =   let open KEDSL in   let reference_fasta =     Machine.get_reference_genome run_with reference_build     |> Reference_genome.fasta in   let name =     sprintf "FreeBayes.bamleftalign %s"       (Filename.basename bam#product#path) in   let clean_up = Remove.file ~run_with output_file_path in   let product =     KEDSL.bam_file       ?sorting:bam#product#sorting       ~reference_build       ~host:(Machine.as_host run_with) output_file_path in   let freebayes = Machine.get_tool run_with Machine.Tool.Default.freebayes in   workflow_node product     ~name     ~make:(Machine.run_big_program run_with ~processors:1 ~name              ~self_ids:["freebayes"; "bamleftalign"]              Program.(                Machine.Tool.(init freebayes)                && shf "cat %s | bamleftalign -c -d -f %s > %s"                  bam#product#path                  reference_fasta#product#path                  output_file_path              ))     ~edges:([         depends_on Machine.Tool.(ensure freebayes);         depends_on bam;         depends_on reference_fasta;         on_failure_activate clean_up;]) end