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