add gene count by default

nf-core · Aug 28, 2023 · 68a9fe1 · 68a9fe1
1 parent f984630
commit 68a9fe1
Showing 1 changed file with 2 additions and 1 deletion.
diff --git 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 {