--- a/csp2_snp.xml	Thu Dec 19 14:51:58 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 15:55:32 2024 -0500
@@ -40,8 +40,8 @@
         export QUERY_READS_ARG="";
 #elif (str($query_reads.query_reads_select) == "collection"):
         #for _, $pair in enumerate($query_reads.coll):
-                ln -sf ${pair.forward} ./queries/${pair.forward.element_identifier};
-                ln -sf ${pair.reverse} ./queries/${pair.reverse.element_identifier};
+                ln -sf ${pair.forward} ./queries/${pair.forward.name};
+                ln -sf ${pair.reverse} ./queries/${pair.reverse.name};
         #end for
         export QUERY_READS_ARG="--reads ./queries";
 #else
@@ -55,8 +55,8 @@
         export REF_READS_ARG="";
 #elif (str($ref_reads.ref_reads_select) == "collection"):
         #for _, $pair in enumerate($ref_reads.coll):
-                ln -sf ${pair.forward} ./references/${pair.forward.element_identifier};
-                ln -sf ${pair.reverse} ./references/${pair.reverse.element_identifier};
+                ln -sf ${pair.forward} ./references/${pair.forward.name};
+                ln -sf ${pair.reverse} ./references/${pair.reverse.name};
         #end for
         export REF_READS_ARG="--ref_reads ./references";
 #else
@@ -162,7 +162,7 @@
                 <param name="trim_name" type="text" value="" label="Text to remove from all file names (e.g., _contigs_skesa)" optional="true" />
                 <param name="rescue" type="boolean" value="false" label="Enable SNP edge rescue mode" optional="true" />
                 <param name="max_missing" type="float" value="50" label="Maximum percent of isolates allowed to have missing data to retain a SNP" optional="true" />
-                <param name="n_ref" type="integer" value="2" label="Number of reference genomes to select" optional="true" />
+                <param name="n_ref" type="integer" value="1" label="Number of reference genomes to select" optional="true" />
 
         </inputs>
         <outputs>