--- a/cfsan_centriflaken.xml	Wed Jul 13 16:28:43 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 16:33:51 2022 -0400
@@ -11,17 +11,16 @@
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
 	    #for _, $unpaired in enumerate($input_read_type_cond.input):
             #if not $unpaired.ext.endswith(('.fastq', '.fastq.gz')):
-                #set read_R1 = str($unpaired.name) + str($unpaired.ext)
+                #set read_R1 = str($unpaired.name) + str('.') + str($unpaired.ext)
             #else:
                 #set read_R1 = str($unpaired.name)
             #end if
-            echo $unpaired.ext
             ln -sf '$unpaired' './cpipes-input/$read_R1';
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
 	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
-	        #set read_R1 = str($pair.forward.name) + str($pair.forward.ext)
-	        #set read_R2 = str($pair.reverse.name) + str($pair.reverse.ext)
+	        #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
+	        #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
 	        ln -sf '$pair.forward' './cpipes-input/$read_R1';
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';
 	    #end for