--- a/cfsan_centriflaken.xml	Tue Jun 28 16:44:58 2022 -0400
+++ b/cfsan_centriflaken.xml	Tue Jun 28 18:18:17 2022 -0400
@@ -6,16 +6,16 @@
     </requirements>    
     <version_command>nextflow -version</version_command>
     <command detect_errors="exit_code"><![CDATA[
-	mkdir -p cpipes-input &&
+	mkdir -p cpipes-input;
 	#for $key in $input.keys()
 	    ln -sf '$input[$key]' './cpipes-input/$key';
 	#end for
-	pwd_path=\$(pwd) &&
+	pwd_path=\$(pwd);
 	$__tool_directory__/0.2.1/cpipes
     #if ($pipeline == "centriflaken"):
         --pipeline $pipeline
         --fq_single_end true
-    #elif ($pipeline.name == "centriflaken_hy"):
+    #elif ($pipeline == "centriflaken_hy"):
         --pipeline $pipeline
         #if ($reads_lib_layout == "single"):
             --fq_single_end true
@@ -61,10 +61,10 @@
     </inputs>
     <outputs>
         <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}">
-            <discover_datasets pattern="__designation_and_ext__" assign_primary_output="true" directory="cpipes-output/${pipeline}-multiqc"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.html" ext="html" assign_primary_output="true" directory="./cpipes-output/${pipeline}-multiqc"/>
         </data>
         <data name="assembled_mags" format="fasta" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
-            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.assembly_filtered_contigs\.(?P&lt;ext&gt;.+)" visible="true" directory="cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
+            <discover_datasets pattern="(?P&lt;designation&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" visible="true" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
         </data>
     </outputs>
     <tests>