--- a/CSP2/nextflow.config	Thu Dec 12 14:04:28 2024 -0500
+++ b/CSP2/nextflow.config	Thu Dec 12 14:15:42 2024 -0500
@@ -17,11 +17,11 @@
     withLabel: 'mummerMem' {
         task_name = 'CSP2-MUMmer'
         cpus = 1
-        # memory = '4 GB'
+        // memory = '4 GB'
     }
     withLabel: 'skesaMem' {
         task_name = 'CSP2-SKESA'
-        # memory = '12 GB'
+        // memory = '12 GB'
     }
 }
 

--- a/csp2_screen.xml	Thu Dec 12 14:04:28 2024 -0500
+++ b/csp2_screen.xml	Thu Dec 12 14:15:42 2024 -0500
@@ -6,59 +6,59 @@
         </requirements>
         <version_command>nextflow -version</version_command>
         <command detect_errors="aggressive"><![CDATA[
-export CSP2_DIR=\$PWD;
-mkdir -p \$CSP2_DIR/queries \$CSP2_DIR/references;
+
+mkdir -p ./queries ./references &&
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
         #for query in $query_fasta:
-                        ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier};
+                ln -sf ${query} ./queries/${query.element_identifier} &&
         #end for
-        export QUERY_FASTA_ARG="--fasta \$CSP2_DIR/queries";
+        export QUERY_FASTA_ARG="--fasta ./queries" &&
 else
-        export QUERY_FASTA_ARG="";
-fi;
+        export QUERY_FASTA_ARG="" &&
+fi &&
 
 if [ -n "$query_reads" ] && [ "$query_reads" != "None" ]; then
         #for query in $query_reads:
-                ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier};
+                ln -sf ${query} \$CSP2_DIR/queries/${query.element_identifier} &&
         #end for
-        export QUERY_READS_ARG="--reads \$CSP2_DIR/queries";
+        export QUERY_READS_ARG="--reads \$CSP2_DIR/queries" &&
 else
-        export QUERY_READS_ARG="";
-fi;
+        export QUERY_READS_ARG="" &&
+fi &&
 
 if [ -n "$ref_fasta" ] && [ "$ref_fasta" != "None" ]; then
         #for ref in $ref_fasta:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier};
+                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
         #end for
-        export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references";
+        export REF_FASTA_ARG="--ref_fasta \$CSP2_DIR/references" &&
 else
-        export REF_FASTA_ARG="";
-fi;
+        export REF_FASTA_ARG="" &&
+fi &&
 
 if [ -n "$ref_reads" ] && [ "$ref_reads" != "None" ]; then
         #for ref in $ref_reads:
-                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier};
+                ln -sf ${ref} \$CSP2_DIR/references/${ref.element_identifier} &&
         #end for
-        export REF_READS_ARG="--ref_reads \$CSP2_DIR/references";
+        export REF_READS_ARG="--ref_reads \$CSP2_DIR/references" &&
 else
-        export REF_READS_ARG="";
-fi;
+        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="";
-fi;
+        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="";
-fi;
+        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_DIR/CSP2_Screen_Output > Nextflow_Log.txt 2>&1;
-cat Nextflow_Log.txt;
+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 &&
+cat Nextflow_Log.txt &&
 ]]>
         </command>
         <inputs>