--- a/csp2_snp.xml	Wed Dec 04 19:08:38 2024 -0500
+++ b/csp2_snp.xml	Thu Dec 05 10:47:01 2024 -0500
@@ -95,20 +95,21 @@
                 <data name="nextflow_log" format="txt" label="Nextflow Log" from_work_dir="Nextflow_Log.txt" />
                 <data name="csp2_zip" format="zip" label="Zipped Output" from_work_dir="CSP2_Output.zip" />
 
-                <collection name="snp_analysis_results" type="list:dataset" label="SNP Analysis Results by Reference ID">
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/CSP2_SNP_Pipeline.log" format="txt" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist.txt" format="txt" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snplist_preserved.txt" format="txt" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Reference_Screening.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Locus_Categories.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/Query_Coverage.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix_preserved.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_matrix.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise_preserved.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snp_distance_pairwise.tsv" format="tabular" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma_preserved.fasta" format="fasta" />
-                        <discover_datasets pattern="CSP2_SNP_Output/SNP_Analysis/*/snpma.fasta" format="fasta" />
+                <collection name="snp_pipeline_output" type="list">
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/CSP2_SNP_Pipeline\.log" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snplist_preserved\.txt" ext="txt" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Reference_Screening\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Locus_Categories\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/Query_Coverage\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_matrix\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise_preserved\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snp_distance_pairwise\.tsv" ext="tabular" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma_preserved\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
+                        <discover_datasets pattern="(?P&lt;reference_id&gt;.+)/snpma\.fasta" ext="fasta" directory="./CSP2_SNP_Output/SNP_Analysis" visible="true" />
                 </collection>
+
         </outputs>
         <tests>
                 <test>