From 68a9fe1c3c6a5d0b47d133633b45283a822468a2 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 28 Aug 2023 12:48:26 +0200
Subject: [PATCH] add gene count by default

---
 conf/modules.config | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/conf/modules.config b/conf/modules.config
index c1e552d5..901957d9 100644
--- a/conf/modules.config
+++ b/conf/modules.config
@@ -352,7 +352,8 @@ process {
         --alignInsertionFlush Right \
         --alignSplicedMateMapLminOverLmate 0 \
         --alignSplicedMateMapLmin 30 \
-        --chimOutType Junctions'
+        --chimOutType Junctions \
+        --quantMode GeneCounts'
     }
 
     withName: STAR_GENOMEGENERATE {