--- a/csp2_snp.xml	Thu Dec 19 14:35:57 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 14:51:58 2024 -0500
@@ -28,8 +28,8 @@
         #for _, $ref_assembly in enumerate($ref_fasta.coll):
                 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
         #end for
-        export REF_FASTA_ARG="--fasta ./queries";
-else
+        export REF_FASTA_ARG="--fasta ./references";
+#else
         #for _, $ref_assembly in enumerate($ref_fasta.list):
                 ln -sf ${ref_assembly} ./references/${ref_assembly.element_identifier};
         #end for
@@ -40,11 +40,11 @@
         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.element_identifier};
+                ln -sf ${pair.reverse} ./queries/${pair.reverse.element_identifier};
         #end for
         export QUERY_READS_ARG="--reads ./queries";
-else
+#else
         #for _, $read_file in enumerate($query_reads.list):
                 ln -sf ${read_file} ./queries/${read_file.element_identifier};
         #end for
@@ -55,11 +55,11 @@
         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.element_identifier};
+                ln -sf ${pair.reverse} ./references/${pair.reverse.element_identifier};
         #end for
         export REF_READS_ARG="--ref_reads ./references";
-else
+#else
         #for _, $read_file in enumerate($ref_reads.list):
                 ln -sf ${read_file} ./references/${read_file.element_identifier};
         #end for