--- a/csp2_screen.xml	Thu Dec 12 16:06:13 2024 -0500
+++ b/csp2_screen.xml	Thu Dec 12 18:30:42 2024 -0500
@@ -7,7 +7,7 @@
         <version_command>nextflow -version</version_command>
         <command detect_errors="aggressive"><![CDATA[
 
-mkdir ./queries ./references ./output;
+mkdir ./queries ./references;
 
 if [ -n "$query_fasta" ] && [ "$query_fasta" != "None" ]; then
         #for query in $query_fasta:
@@ -58,10 +58,7 @@
 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 &&
-ls -la CSP2_Screen_Output &&
-sleep 5 &&
-ls -la CSP2_Screen_Output &&
-cp CSP2_Screen_Output/Screening_Results.tsv CSP2_Screen_Output/Raw_MUMmer_Summary.tsv CSP2_Screen_Output/Isolate_Data.tsv output/;
+ls -la CSP2_Screen_Output;
 ]]>
         </command>
         <inputs>
@@ -83,9 +80,9 @@
                 <param name="ref_id" type="text" value="" label="Comma-separated list of desired Reference IDs (e.g., Sample_A,Sample_B)" optional="true" />
         </inputs>
         <outputs>
-                <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="output/Raw_MUMmer_Summary.tsv" />
-                <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="output/Isolate_Data.tsv" />
-                <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="output/Screening_Results.tsv" />
+                <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_Screen_Output/Raw_MUMmer_Summary.tsv" />
+                <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_Screen_Output/Isolate_Data.tsv" />
+                <data name="screening_results" format="tabular" label="Screening Results" from_work_dir="CSP2_Screen_Output/Screening_Results.tsv" />
         </outputs>
         <tests>
                 <test>