# HG changeset patch
# User kkonganti
# Date 1656510458 14400
# Node ID 05b6b4edfd58e9ebc0e7369ca440396ad727e72e
# Parent  4774fc77e872c7e16b59b1fae8ee181f6efbe147
"planemo upload"

diff -r 4774fc77e872 -r 05b6b4edfd58 cfsan_centriflaken.xml
--- a/cfsan_centriflaken.xml	Wed Jun 29 09:40:21 2022 -0400
+++ b/cfsan_centriflaken.xml	Wed Jun 29 09:47:38 2022 -0400
@@ -32,7 +32,8 @@
 	--flye_genome_size '${genome_size}'
 	-profile $runtime_profile
     -resume;
-    cp cpipes-output/${pipeline}-multiqc/multiqc_report.html multiqc_report.html;
+    mv './cpipes-output/${pipeline}-multiqc/multiqc_report.html' './multiqc_report.html';
+    mv './cpipes-output/${pipeline}-results/kraken2_extract_contigs' kraken2_extract_contigs;
     ]]></command>
     <inputs>
         <param name="input" type="data_collection" collection_type="list" format="fastq,fastq.gz,fastqsanger.gz,fastqsanger" label="Input read collection" />
@@ -63,7 +64,7 @@
     <outputs>
         <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"/>
+            <discover_datasets pattern="(?P&lt;name&gt;.*)\.assembly_filtered_contigs\.fasta" ext="fasta" directory="kraken2_extract_contigs"/>
         </collection>
     </outputs>
     <tests>