Commit 21ff28bf authored by Jerome Mariette's avatar Jerome Mariette
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parent 9897c125
......@@ -163,7 +163,7 @@ class MothurMakeContigs(Analysis):
,cmd_format='{EXE} {IN} {OUT}')
makecontigs(inputs=[self.stability_files],includes=[self.read1_files, self.read2_files],outputs=[self.stdout,self.trim_fasta_files,self.scrap_fasta_files,self.groups_files,\
self.report_files])
screenseqs = ShellFunction(self.get_exec_path("mothur") + ' "#screen.seqs(fasta=$1,group=$2,maxambig='+self.maxambig+',maxlength='+self.maxlength+\
screenseqs = ShellFunction(self.get_exec_path("mothur") + ' "#screen.seqs(fasta=$1,group=$2,maxambig='+str(self.maxambig)+',maxlength='+str(self.maxlength)+\
',outputdir='+self.output_directory+'/,processors='+str(self.processors)+')" > $3',cmd_format='{EXE} {IN} {OUT}')
screenseqs = MultiMap(screenseqs, inputs=[self.trim_fasta_files,self.groups_files],outputs=[self.stdout_screenseqs,self.good_fasta_files,self.bad_accnos_files,\
self.good_groups_files])
\ No newline at end of file
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