# HG changeset patch
# User kkonganti
# Date 1657747084 14400
# Node ID 7e421f421b5e54e4967a9abb961d002d6147c3eb
# Parent  022230c283f2703e62b209b507dd824501474960
"planemo upload"

diff -r 022230c283f2 -r 7e421f421b5e cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jul 13 17:02:56 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jul 13 17:18:04 2022 -0400
@@ -8,6 +8,7 @@
     <command detect_errors="exit_code"><![CDATA[
 	mkdir -p cpipes-input || exit 1;
     pwd_path=\$(pwd);
+    #import re
     #if (str($input_read_type_cond.input_read_type) == "single_long"):
 	    #for _, $unpaired in enumerate($input_read_type_cond.input):
             #set read1 = str($unpaired.name)
@@ -18,13 +19,13 @@
 	    #end for
     #elif (str($input_read_type_cond.input_read_type) == "paired"):
 	    #for _, $pair in enumerate($input_read_type_cond.input_pair)
-            #set read_R1 = str($pair.forward.name)
-            #set read_R2 = str($pair.reverse.name)
+            #set read_R1 = re.sub('\:forward', '_forward', str($pair.forward.name))
+            #set read_R2 = re.sub('\:reverse', '_reverse', str($pair.reverse.name))
             #if not str($pair.forward.name).endswith(('.fastq', '.fastq.gz')):
-	            #set read_R1 = str($pair.forward.name) + str('.') + str($pair.forward.ext)
+	            #set read_R1 = $read_R1 + str('.') + str($pair.forward.ext)
             #end if
             #if not str($pair.reverse.name).endswith(('.fastq', '.fastq.gz')):
-                #set read_R2 = str($pair.reverse.name) + str('.') + str($pair.reverse.ext)
+                #set read_R2 = $read_R2 + str('.') + str($pair.reverse.ext)
             #end if
 	        ln -sf '$pair.forward' './cpipes-input/$read_R1';
 	        ln -sf '$pair.reverse' './cpipes-input/$read_R2';