# HG changeset patch
# User greg
# Date 1606167754 0
# Node ID 6116deacb2c7f844fc905bb103b8dd2011a54aaf
# Parent  ee6166a3edd8ad4165103b4c31592c3b63905b19
Uploaded

diff -r ee6166a3edd8 -r 6116deacb2c7 vsnp_determine_ref_from_data.xml
--- a/vsnp_determine_ref_from_data.xml	Thu Nov 19 21:50:54 2020 +0000
+++ b/vsnp_determine_ref_from_data.xml	Mon Nov 23 21:42:34 2020 +0000
@@ -34,12 +34,23 @@
         #end if
     #end if
 #else:
+    #set collection_type = $input_type_cond.collection_type_cond.collection_type
     #for $i in $input_type_cond.collection_type_cond.reads_collection:
         #if $i.is_of_type('fastqsanger.gz'):
             #set gzipped = 'true'
         #end if
         #set filename = $i.file_name
-        #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #if str($collection_type) == 'single_reads':
+            #set identifier = re.sub('[^\s\w\-]', '_', str($i.element_identifier))
+        #else:
+            ## Galaxy builds lists of pairs as nested lists with elements
+            ## named forward and reverse.  When flattened, these lists
+            ## will work as inputs to the Parse parameter value expression
+            ## tool in workflows.  However, the output list created by the
+            ## expression tool will not function correctly with the bwa_mem
+            ## mapper.  Naming the identifier as follows is a solution.
+            #set identifier = re.sub('[^\s\w\-]', '_', str($i.name))
+        #end if
         ln -s '$filename' '$input_reads_dir/$identifier' &&
     #end for
 #end if