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workflows/miseq_diversity/__init__.py

@@ -142,6 +142,7 @@ class MiSeqDiversity (NG6Workflow):
 											'reference_alignment_files':alignment_template,
 											'count_table_files':countseqs.count_table_files, 
 											'maxhomop':self.args["max_homopolymers"],
+											'maxambig':self.args["max_ambiguous"],
 											'processors':self.args["processors"]}, 
 										parent=makecontigs)