--- a/csp2_snp.xml	Thu Dec 19 13:02:58 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 19 13:20:18 2024 -0500
@@ -20,6 +20,12 @@
 export REF_FASTA_SELECT="$ref_fasta.ref_fasta_select"
 export REF_READS_SELECT="$ref_reads.ref_reads_select"
 
+echo "Query Fasta: \$QUERY_FASTA_SELECT";
+echo "Ref Fasta: \$REF_FASTA_SELECT";
+
+echo "Query Reads: \$QUERY_READS_SELECT";
+echo "Ref Reads: \$REF_READS_SELECT";
+
 if [[ "\$QUERY_FASTA_SELECT" == 'collection' ]]; then
     #set query_fasta_input=$query_fasta.coll.elements
 elif [[ "\$QUERY_FASTA_SELECT" == 'history' ]]; then
@@ -42,17 +48,11 @@
 if [[ "\$REF_READS_SELECT" == 'collection' ]]; then
     #set ref_reads_forward=$ref_reads.coll.forward
     #set ref_reads_reverse=$ref_reads.coll.reverse
-elif [[ "\$REF_READS_SELECT" =='history' ]]; then
+elif [[ "\$REF_READS_SELECT" == 'history' ]]; then
     #set ref_reads_forward=$ref_reads.list
 fi;
 
-echo "Query Fasta: \$QUERY_FASTA_SELECT";
-echo "Ref Fasta: \$REF_FASTA_SELECT";
-
-echo "Query Reads: \$QUERY_READS_SELECT";
-echo "Ref Reads: \$REF_READS_SELECT";
-
-if [[ "\$QUERY_FASTA_SELECT" == 'none']]; then
+if [[ "\$QUERY_FASTA_SELECT" == 'none' ]]; then
         export QUERY_FASTA_ARG="";
 else
         #for query in $query_fasta_input:
@@ -61,8 +61,7 @@
         export QUERY_FASTA_ARG="--fasta ./queries";
 fi;
 
-
-if [[ "$ref_fasta.ref_fasta_select" == "none" ]]; then
+if [[ "\$REF_FASTA_SELECT" == "none" ]]; then
         export REF_FASTA_ARG="";
 else
         #for ref in $ref_fasta_input:
@@ -71,7 +70,7 @@
         export REF_FASTA_ARG="--fasta ./references";
 fi;
 
-if [[ "$query_reads.query_reads_select" == "none" ]]; then
+if [[ "\$QUERY_READS_SELECT" == "none" ]]; then
         export QUERY_READS_ARG="";
 else
         #for query in $query_reads_forward $query_reads_reverse:
@@ -80,7 +79,7 @@
         export QUERY_READS_ARG="--reads ./queries";
 fi;
 
-if [[ "$ref_reads.ref_reads_select" == "none" ]]; then
+if [[ "\$REF_READS_SELECT" == "none" ]]; then
         export QUERY_READS_ARG="";
 else
         #for ref in $ref_reads_forward $ref_reads_reverse: