--- a/csp2_snp.xml	Thu Dec 05 18:09:26 2024 -0500
+++ b/csp2_snp.xml	Fri Dec 06 08:08:22 2024 -0500
@@ -59,7 +59,6 @@
 
 nextflow run ${__tool_directory__}/CSP2/CSP2.nf -profile csp2_galaxy --runmode snp \$QUERY_FASTA_ARG \$REF_FASTA_ARG \$QUERY_READS_ARG \$REF_READS_ARG \$TRIM_ARG \$RESCUE_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 --max_missing $max_missing --out \$CSP2_DIR/CSP2_SNP_Output > Nextflow_Log.txt 2>&1;
 
-mkdir -p Output; for file in CSP2_SNP_Output/SNP_Analysis/*/*; do ln -sf "\$file" Output/; done;
 zip -r CSP2_Output.zip CSP2_SNP_Output;
 ]]>
         </command>
@@ -86,12 +85,14 @@
                 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
                 <data name="isolate_data" format="tabular" label="Isolate Data" from_work_dir="CSP2_SNP_Output/Isolate_Data.tsv" />
                 <data name="raw_mummer" format="tabular" label="Raw MUMmer Output" from_work_dir="CSP2_SNP_Output/Raw_MUMmer_Summary.tsv" />
-                <data name="reference_screening" format="tabular" label="Reference Screening Data" from_work_dir="Output/Reference_Screening.tsv" />
-                <data name="csp2_log" format="txt" label="CSP2 Log" from_work_dir="Output/CSP2_SNP_Pipeline.log" />
-                <data name="snp_matrix" format="tabular" label="Preserved SNP Matrix" from_work_dir="Output/snp_distance_matrix_preserved.tsv" />
-                <data name="snp_pairwise" format="tabular" label="Preserved SNP Pairwise Distances" from_work_dir="Output/snp_distance_pairwise_preserved.tsv" />
-                <data name="snp_alignment" format="fasta" label="Preserved SNP Alignment" from_work_dir="Output/snpma_preserved.fasta" />
                 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
+                <collection name="reference_results" type="list:list">
+                        <discover_datasets pattern="*/CSP2_SNP_Pipeline.log" format="txt" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                        <discover_datasets pattern="*/Reference_Screening.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                        <discover_datasets pattern="*/snp_distance_matrix_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                        <discover_datasets pattern="*/snp_distance_pairwise_preserved.tsv" format="tabular" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                        <discover_datasets pattern="*/snpma_preserved.fasta" format="fasta" visible="true" directory="./CSP2_SNP_Output/SNP_Analysis" />
+                </collection>
         </outputs>
         <tests>
                 <test>