# HG changeset patch
# User kkonganti
# Date 1656509598 14400
# Node ID 91480ddc3fcd70d7c3477cb6105bf813e3cc4c29
# Parent  2671e2d54a254dceedfa680f9c618e598431aca5
"planemo upload"

diff -r 2671e2d54a25 -r 91480ddc3fcd cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jun 29 09:15:39 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jun 29 09:33:18 2022 -0400
@@ -31,7 +31,8 @@
 	--centrifuge_extract_bug '${centrifuge_extract_bug}'
 	--flye_genome_size '${genome_size}'
 	-profile $runtime_profile
-    -resume
+    -resume;
+    cp ./cpipes-output/${pipeline}-multiqc/multiqc_report.html .;
     ]]></command>
     <inputs>
         <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
@@ -60,7 +61,7 @@
         </param>
     </inputs>
     <outputs>
-        <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="./cpipes-output/${pipeline}-multiqc/multiqc_report.html"/>
+        <data name="multiqc_report" format="html" label="MultiQC Report on ${on_string}" from_work_dir="multiqc_report.html"/>
         <collection name="assembled_mags" type="list" label="CENTRIFLAKEN: Assembled MAGs on ${on_string}">
             <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" directory="./cpipes-output/${pipeline}-results/kraken2_extract_contigs"/>
         </collection>