--- a/csp2_screen.xml	Thu Dec 12 14:30:01 2024 -0500
+++ b/csp2_screen.xml	Thu Dec 12 14:47:33 2024 -0500
@@ -11,50 +11,50 @@
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
         #for query in $query_fasta:
-                ln -sf ${query} ./queries/${query.element_identifier} &&
+                ln -sf ${query} ./queries/${query.element_identifier};
         #end for
-        export QUERY_FASTA_ARG="--fasta ./queries" &&
+        export QUERY_FASTA_ARG="--fasta ./queries";
 else
-        export QUERY_FASTA_ARG="" &&
+        export QUERY_FASTA_ARG="";
 fi;
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
         #for query in $query_reads:
-                ln -sf ${query} ./queries/${query.element_identifier} &&
+                ln -sf ${query} ./queries/${query.element_identifier};
         #end for
-        export QUERY_READS_ARG="--reads ./queries" &&
+        export QUERY_READS_ARG="--reads ./queries";
 else
-        export QUERY_READS_ARG="" &&
+        export QUERY_READS_ARG="";
 fi;
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
         #for ref in $ref_fasta:
-                ln -sf ${ref} ./references/${ref.element_identifier} &&
+                ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_FASTA_ARG="--ref_fasta ./references" &&
+        export REF_FASTA_ARG="--ref_fasta ./references";
 else
-        export REF_FASTA_ARG="" &&
+        export REF_FASTA_ARG="";
 fi;
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
         #for ref in $ref_reads:
-                ln -sf ${ref} ./references/${ref.element_identifier} &&
+                ln -sf ${ref} ./references/${ref.element_identifier};
         #end for
-        export REF_READS_ARG="--ref_reads ./references" &&
+        export REF_READS_ARG="--ref_reads ./references";
 else
-        export REF_READS_ARG="" &&
+        export REF_READS_ARG="";
 fi;
 
 if [ -n "$trim_name" ] && [ "$trim_name" != "None" ]; then
-        export TRIM_ARG="--trim_name $trim_name" &&
+        export TRIM_ARG="--trim_name $trim_name";
 else
-        export TRIM_ARG="" &&
+        export TRIM_ARG="";
 fi;
 
 if [ -n "$ref_id" ] && [ "$ref_id" != "None" ]; then
-        export REF_ID_ARG="--ref_id $ref_id" &&
+        export REF_ID_ARG="--ref_id $ref_id";
 else
-        export REF_ID_ARG="" &&
+        export REF_ID_ARG="";
 fi;
 
 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode screen \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$REF_ID_ARG \$TRIM_ARG --readext $readext --forward $forward --reverse $reverse --ref_readext $readext --ref_forward $forward --ref_reverse $reverse --min_cov $min_cov --min_iden $min_iden --min_len $min_len --ref_edge $ref_edge --query_edge $query_edge --dwin $dwin --wsnps $wsnps --out ./CSP2_Screen_Output > Nextflow_Log.txt 2>&1;