From 5db450b7b5dd2fe3d2077dd58630b0a1a1e31a39 Mon Sep 17 00:00:00 2001
From: "Thomas A. Christensen II" <25492070+MillironX@users.noreply.github.com>
Date: Tue, 14 Jun 2022 08:48:16 -0500
Subject: [PATCH] Add output configuration for Kraken Krona chart

---
 conf/modules.config | 8 ++++++++
 1 file changed, 8 insertions(+)

diff --git a/conf/modules.config b/conf/modules.config
index 46320cf..2ea2f1f 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -293,6 +293,14 @@ process {
         ]
     }
 
+    withName: KRONA_IMPORTKRAKEN {
+        publishDir = [
+            path: { "${params.outdir}/krona" },
+            mode: params.publish_dir_mode,
+            pattern: '*.{html}'
+        ]
+    }
+
     withName: METAPHLAN3 {
         ext.args = { "${meta.db_params}" }
         ext.prefix = params.perform_runmerging ? { "${meta.id}-${meta.db_name}" } : { "${meta.id}-${meta.run_accession}-${meta.db_name}" }