Methylseq

workflows/methylseq/components/remove_duplicate.py

@@ -42,12 +42,12 @@ class RemoveDuplicate (Analysis):
         if self.get_memory() != None :
             self.mem=self.get_memory()
         self.add_output_file_list("flagstat_init", "Flagstat initialy", pattern='{basename_woext}.init_flagstat', items=self.bam)
-        self.add_output_file_list("flagstat_rmdup", "Flagstat result after rmdup", pattern='{basename_woext}.rmdup_flagstat', items=self.bam)
         self.add_output_file_list("flagstat_finally", "Flagstat result after removing singleton", pattern='{basename_woext}.finally_flagstat', items=self.bam)
-
+        if self.is_paired:
+            self.add_output_file_list("flagstat_rmdup", "Flagstat result after rmdup", pattern='{basename_woext}.rmdup_flagstat', items=self.bam)
+            self.add_output_file_list("rmdup_stderr", "The error trace file", pattern='{basename_woext}_rmdup.stderr', items=self.bam)       
         self.add_output_file_list("output", "The bam with removed duplicates (and singleton if paired)", pattern='{basename_woext}_clean.bam', items=self.bam)
         
-        self.add_output_file_list("rmdup_stderr", "The error trace file", pattern='{basename_woext}_rmdup.stderr', items=self.bam)
         self.add_output_file_list("rmsinglet_stderr","The error trace file", pattern='{basename_woext}_rmsinglet.stderr', items=self.bam)
     
     def define_analysis(self):