val run_gen_cmd : ?mlst_db:Defs.fasta Bistro.Std.workflow ‑> ?mlst_delimiter:string ‑> ?mlst_definitions:Defs.fasta Bistro.Std.workflow ‑> ?mlst_max_mismatch:int ‑> ?gene_db:Defs.fasta Bistro.Std.workflow list ‑> ?no_gene_details:bool ‑> ?gene_max_mismatch:int ‑> ?min_coverage:int ‑> ?max_divergence:int ‑> ?min_depth:int ‑> ?min_edge_depth:int ‑> ?prob_err:float ‑> ?truncation_score_tolerance:int ‑> ?other:string ‑> ?max_unaligned_overlap:int ‑> ?mapq:int ‑> ?baseq:int ‑> ?samtools_args:string ‑> ?report_new_consensus:bool ‑> ?report_all_consensus:bool ‑> string ‑> Bistro.Template.t list ‑> Bistro.EDSL.commandval run_se : ?mlst_db:Defs.fasta Bistro.Std.workflow ‑> ?mlst_delimiter:string ‑> ?mlst_definitions:Defs.fasta Bistro.Std.workflow ‑> ?mlst_max_mismatch:int ‑> ?gene_db:Defs.fasta Bistro.Std.workflow list ‑> ?no_gene_details:bool ‑> ?gene_max_mismatch:int ‑> ?min_coverage:int ‑> ?max_divergence:int ‑> ?min_depth:int ‑> ?min_edge_depth:int ‑> ?prob_err:float ‑> ?truncation_score_tolerance:int ‑> ?other:string ‑> ?max_unaligned_overlap:int ‑> ?mapq:int ‑> ?baseq:int ‑> ?samtools_args:string ‑> ?report_new_consensus:bool ‑> ?report_all_consensus:bool ‑> ?threads:int ‑> 'a Defs.fastq Bistro.Std.workflow list ‑> [ `srst2 ] Bistro.Std.directory Bistro.Std.workflowval run_pe : ?mlst_db:Defs.fasta Bistro.Std.workflow ‑> ?mlst_delimiter:string ‑> ?mlst_definitions:Defs.fasta Bistro.Std.workflow ‑> ?mlst_max_mismatch:int ‑> ?gene_db:Defs.fasta Bistro.Std.workflow list ‑> ?no_gene_details:bool ‑> ?gene_max_mismatch:int ‑> ?min_coverage:int ‑> ?max_divergence:int ‑> ?min_depth:int ‑> ?min_edge_depth:int ‑> ?prob_err:float ‑> ?truncation_score_tolerance:int ‑> ?other:string ‑> ?max_unaligned_overlap:int ‑> ?mapq:int ‑> ?baseq:int ‑> ?samtools_args:string ‑> ?report_new_consensus:bool ‑> ?report_all_consensus:bool ‑> ?threads:int ‑> 'a Defs.fastq Bistro.Std.workflow list ‑> [ `srst2 ] Bistro.Std.directory Bistro.Std.workflow