From 724f7e2c8494b51f58e261b1cebdfa0c628e05db Mon Sep 17 00:00:00 2001
From: Robrecht Cannoodt <rcannood@gmail.com>
Date: Mon, 26 Feb 2024 12:22:16 +0100
Subject: [PATCH] add TODOs

---
 src/star/star_align/test.sh | 9 +++++++++
 1 file changed, 9 insertions(+)

diff --git a/src/star/star_align/test.sh b/src/star/star_align/test.sh
index 76c2a534..20c5488e 100644
--- a/src/star/star_align/test.sh
+++ b/src/star/star_align/test.sh
@@ -80,4 +80,13 @@ echo ">> Check if output exists"
 cd ..
 #########################################################################################
 
+# TODO: check whether optional outputs work: 
+#   - quantMode "TranscriptomeSAM;GeneCounts"
+#   - reads_per_gene "reads_per_gene.tsv"
+#   - chimOutType "Junctions"
+#   - chimeric_junctions "chimeric_junctions.tsv"
+#   - outSJtype Standard
+#   - splice_junctions "splice_junctions.tsv"
+# TODO: check whether output contents are correct
+
 echo "> Test successful"
\ No newline at end of file