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workflows/miseq_diversity/components/mothurmakecontigs.py

@@ -51,10 +51,8 @@ class MothurMakeContigs(Analysis):
             else : self.reverse_primer = None
             self.oligos_file = os.path.join(self.output_directory, 'oligos.oligos')
         else : self.oligos_file = None
-        if maxambig : self.maxambig = maxambig
-        else : self.maxambig = None
-        if maxlength : self.maxlength = maxlength
-        else : self.maxlength = None
+        self.maxambig = maxambig
+        self.maxlength = maxlength
         self.pdiffs = pdiffs
         self.processors = processors
         # define input files
@@ -89,7 +87,7 @@ class MothurMakeContigs(Analysis):
             self.options = '#make.contigs(file=stability.file,oligos=oligos.oligos,pdiffs='+str(self.pdiffs)+');'
         else:
             self.options = '#make.contigs(file=stability.file);'
-        self.options += '#screen.seqs(fasta=FILE.fasta,group=FILE.groups,maxambig='+self.maxambig+',maxlength='+self.maxlength+');'
+        self.options += '#screen.seqs(fasta=FILE.fasta,group=FILE.groups,maxambig='+str(self.maxambig)+',maxlength='+str(self.maxlength)+');'
     
     def get_version(self):
         cmd = [self.get_exec_path("mothur"), "-version"]