# HG changeset patch
# User kkonganti
# Date 1657736436 14400
# Node ID 61b7ab692529d5a4d25409c23b12eb49796679fb
# Parent  306431b9bf869c4fe544bc6ab3cece227b0c3090
"planemo upload"

diff -r 306431b9bf86 -r 61b7ab692529 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 14:17:13 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 14:20:36 2022 -0400
@@ -8,17 +8,14 @@
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
-    #import os
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
 	    #for $key in $input_read_type_cond.input.keys()
 	        ln -sf '$input_read_type_cond.input[$key]' './cpipes-input/$key';
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
         #for _, $pair in enumerate($input_read_type_cond.input_pair)
-            #set $read_R1 = os.path.basename(str($pair.forward))
-            #set $read_R2 = os.path.basename(str($pair.reverse))
-            #set $read_R1_name = str($read_R1.name)
-            #set $read_R2_name = str($read_R2.name)
+            #set read_R1_name = str($pair.forward.name)
+            #set read_R2_name = str($pair.reverse.name)
 	        ln -sf '$pair.forward' './cpipes-input/$read_R1_name';
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2_name';
 	    #end for