let run     ~run_with ~normal ~tumor ~result_prefix ?(more_edges = [])     ?(configuration = Configuration.default) () =   let open KEDSL in   let open Configuration in   let name = Filename.basename result_prefix in   let result_file suffix = result_prefix ^ suffix in   let output_dir = result_file "strelka_output" in   let config_file_path = result_file  "configuration" in   let output_file_path = output_dir // "results/passed_somatic_combined.vcf" in   let reference_fasta =     Machine.get_reference_genome run_with normal#product#reference_build     |> Reference_genome.fasta in   let strelka_tool = Machine.get_tool run_with Machine.Tool.Default.strelka in   let gatk_tool = Machine.get_tool run_with Machine.Tool.Default.gatk in   let sorted_normal =     Samtools.sort_bam_if_necessary       ~run_with ~by:`Coordinate normal in   let sorted_tumor =     Samtools.sort_bam_if_necessary       ~run_with ~by:`Coordinate tumor in   let working_dir = Filename.(dirname result_prefix) in   let processors = Machine.max_processors run_with in   let make =     Machine.run_big_program run_with ~name ~processors       ~self_ids:["strelka"]       Program.(         Machine.Tool.init strelka_tool && Machine.Tool.init gatk_tool         && shf "mkdir -p %s"  working_dir         && shf "cd %s" working_dir         && generate_config_file ~path:config_file_path configuration         && shf "rm -fr %s" output_dir (* strelka won't start if this                                          directory exists *)         && shf "$STRELKA_BIN/configureStrelkaWorkflow.pl            --normal=%s                 --tumor=%s                  --ref=%s                   --config=%s                 --output-dir=%s "           sorted_normal#product#path           sorted_tumor#product#path           reference_fasta#product#path           config_file_path           output_dir         && shf "cd %s" output_dir         && shf "make -j%d" processors         && Gatk.call_gatk ~analysis:"CombineVariants" [           "--variant:snvs"; "results/passed.somatic.snvs.vcf";           "--variant:indels"; "results/passed.somatic.indels.vcf";           "-R"; reference_fasta#product#path;           "-genotypeMergeOptions"; "PRIORITIZE";           "-o"; output_file_path; "-priority"; "snvs,indels"         ]       )   in   workflow_node ~name ~make     (vcf_file output_file_path        ~reference_build:normal#product#reference_build        ~host:Machine.(as_host run_with))     ~edges:(more_edges @ [         depends_on normal;         depends_on tumor;         depends_on reference_fasta;         depends_on (Machine.Tool.ensure strelka_tool);         depends_on (Machine.Tool.ensure gatk_tool);         depends_on sorted_normal;         depends_on sorted_tumor;         depends_on (Picard.create_dict ~run_with reference_fasta);         depends_on (Samtools.faidx ~run_with reference_fasta);         depends_on (Samtools.index_to_bai ~run_with sorted_normal);         depends_on (Samtools.index_to_bai ~run_with sorted_tumor);       ])