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workflows/r454_diversity/__init__.py

@@ -42,17 +42,15 @@ class RNAdiversity (Workflow):
    		trimseqs = self.add_component("MothurTrimSeqs",[shhhflows.fasta_files, oligos_fullpath, shhhflows.names_files])
 		uniqueseqs = self.add_component("MothurUniqueSeqs",[trimseqs.trim_fasta_files, trimseqs.trim_names_files])
 		alignseqs = self.add_component("MothurAlignSeqs",[uniqueseqs.unique_fasta_files,self.args["reference_alignment"]])
-		
+		summaryseqs_align = self.add_component("MothurSummarySeqs", [alignseqs.align_files,uniqueseqs.unique_names_files],component_prefix="align")	
+
 		#screenseqs = self.add_component("MothurScreenSeqs",[alignseqs.align_files,uniqueseqs.names_files,trimseqs.groups_files])
-		#summaryseqs_screen = self.add_component("MothurSummarySeqs", [screenseqs.good_align_files,screenseqs.good_names_files],{},"screen")	
 		#filterseqs = self.add_component("MothurFilterSeqs",[screenseqs.good_align_files])
 		#uniqueseqs_filter = self.add_component("MothurUniqueSeqs",[filterseqs.filter_fasta_files,screenseqs.good_names_files],{},"filter")
 		#precluster = self.add_component("MothurPreCluster",[uniqueseqs_filter.unique_fasta_files,uniqueseqs_filter.names_files,screenseqs.good_groups_files])
-		#summaryseqs_precluster = self.add_component("MothurSummarySeqs", [precluster.precluster_fasta_files,precluster.precluster_names_files],{},"precluster")
 		#chimerauchime = self.add_component("MothurChimeraUchime",[precluster.precluster_fasta_files,precluster.precluster_names_files,screenseqs.good_groups_files])
 		#removeseqs = self.add_component("MothurRemoveSeqs",[chimerauchime.uchime_accnos_files,precluster.precluster_fasta_files,precluster.precluster_names_files,\
 		#												screenseqs.good_groups_files])
-		#summaryseqs_removeseqs = self.add_component("MothurSummarySeqs", [removeseqs.pick_fasta_files,removeseqs.pick_names_files],{},"removeseqs")
 		#classifyseqs = self.add_component("MothurClassifySeqs",[removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,self.args["template"],\
 		#														self.args["taxonomy"]])
 #   		removegroups = self.add_component("MothurRemoveGroups", [removeseqs.pick_fasta_files,removeseqs.pick_names_files,removeseqs.pick_groups_files,classifyseqs.taxonomy_files])

workflows/r454_diversity/components/mothursummaryseqs.py

@@ -27,7 +27,7 @@ class MothurSummarySeqs(Component):
         if names_files:
             self.names_files = InputFileList(self.names_files, Formats.MOTHUR_NAMES)
         #define output files
-        self.summary_files = OutputFileList(self.get_outputs('{basename_woext}.summary', self.fasta_files), Formats.MOTHUR_SUMMARY)
+        self.summary_files = OutputFileList(self.get_outputs('{basename_woext}.summary', self.fasta_files))
         self.stdout = OutputFileList(self.get_outputs('{basename_woext}.stdout', self.fasta_files))
 
     def process(self):