From 9500726e4dcb1a6204c04dd1a80228221838383c Mon Sep 17 00:00:00 2001
From: "James A. Fellows Yates" <jfy133@gmail.com>
Date: Wed, 11 Sep 2024 02:50:25 +0000
Subject: [PATCH] Drop unnecesary ganon parameter (should come via db_params)
 and pattern for classify to 2.0 valid,

---
 conf/modules.config | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/conf/modules.config b/conf/modules.config
index ff0f79c1..d298a828 100644
--- 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}'
         ]
     }