Drop unnecesary ganon parameter (should come via db_params) and patte…

…rn for classify to 2.0 valid,
nf-core · Sep 11, 2024 · 9500726 · 9500726
1 parent af8bc72
commit 9500726
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -808,12 +808,12 @@ process {
 
     withName: GANON_CLASSIFY {
         tag = {"${meta.db_name}|${meta.id}"}
-        ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all -m lca --output-unclassified" } : { "${meta.db_params}" }
+        ext.args = params.ganon_save_readclassifications ? { "${meta.db_params} --output-all --output-unclassified" } : { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}_${meta.db_name}.ganon" } : { "${meta.id}_${meta.run_accession}_${meta.db_name}.ganon" }
         publishDir = [
             path: { "${params.outdir}/ganon/${meta.db_name}/" },
             mode: params.publish_dir_mode,
-            pattern: '*.{tre,rep,lca,all,unc,log}'
+            pattern: '*.{tre,rep,one,all,unc,log}'
         ]
     }