Mercurial > repos > kkonganti > cfsan_centriflaken

changeset 24:05b6b4edfd58

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"planemo upload"
author kkonganti
date Wed, 29 Jun 2022 09:47:38 -0400
parents 4774fc77e872
children b9cd7722d51b
files cfsan_centriflaken.xml
diffstat 1 files changed, 3 insertions(+), 2 deletions(-) [+]
line wrap: on
line diff
--- 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>