From d53112c7f7a0df8e73cba5d5d81e99095d9eef1e Mon Sep 17 00:00:00 2001
From: Leon Hafner <leon.hafner@tum.de>
Date: Fri, 13 Sep 2024 14:17:23 +0200
Subject: [PATCH] add BAM file output

---
 assets/end_to_end.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/assets/end_to_end.py b/assets/end_to_end.py
index cf1cfd9..3c8f46e 100644
--- a/assets/end_to_end.py
+++ b/assets/end_to_end.py
@@ -165,6 +165,7 @@ def list_files_recursive(directory):
     --gtf {gtf} \
     --fasta {fasta} \
     --read_length 50 \
+    --save_align_intermeds \
     -profile {profile} \
     -process.executor {process_executor} \
     -resume \