--- a/cfsan_centriflaken.xml	Tue Jun 28 15:13:05 2022 -0400
+++ b/cfsan_centriflaken.xml	Tue Jun 28 16:44:58 2022 -0400
@@ -61,10 +61,10 @@
     </inputs>
     <outputs>
         <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}">
-            <discover_datasets pattern="multiqc_report.html" assign_primary_output="true" directory="cpipes-output/${pipeline}-multiqc"/>
+            <discover_datasets pattern="__designation_and_ext__" assign_primary_output="true" directory="cpipes-output/${pipeline}-multiqc"/>
         </data>
         <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
-            <discover_datasets pattern=".*\.assembly_filtered_contigs.fasta" visible="true" directory="cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.assembly_filtered_contigs\.(?P&lt;ext&gt;.+)" visible="true" directory="cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
         </data>
     </outputs>
     <tests>