diff --git a/tests/data_1/shotgun_test.sh b/tests/data_1/shotgun_test.sh
index b57e539..f74788e 100755
--- a/tests/data_1/shotgun_test.sh
+++ b/tests/data_1/shotgun_test.sh
@@ -1,4 +1,4 @@
 #!/bin/bash
 
 viloca run -a 0.1 -w 201 --mode shorah -x 100000 -p 0.9 -c 0 \
--r HXB2:2469-3713 -R 42 -f test_ref.fasta -b test_aln.cram --out_format csv "$@"
+-r HXB2:2469-3713 -R 42 -f ../test_ref.fasta -b ../test_aln.cram --out_format csv "$@"
diff --git a/tests/test_shotgun_e2e.py b/tests/test_shotgun_e2e.py
index 6457f88..79aed71 100644
--- a/tests/test_shotgun_e2e.py
+++ b/tests/test_shotgun_e2e.py
@@ -27,22 +27,31 @@ def run(base_files):
     run(base_files)
 
 def test_e2e_shorah():
+    cwd_test_e2e = "./data_1/test_e2e_shorah"
+    # Check if the directory exists, if not, create it
+    if not os.path.exists(cwd_test_e2e):
+        os.makedirs(cwd_test_e2e)
+
     original = subprocess.run(
-        "./shotgun_test.sh", shell=True, check=True, cwd=cwd
+        "../shotgun_test.sh", shell=True, check=True, cwd=cwd_test_e2e
     )
     assert original.returncode == 0
     assert os.path.isfile(os.path.join(cwd, f_path)) == False
 
     assert filecmp.cmp(
         "./data_1/test.csv",
-        "./data_1/work/snv/SNVs_0.010000_final.csv",
+        "./data_1/test_e2e_shorah/work/snv/SNVs_0.010000_final.csv",
         shallow=False
     )
 
 def test_e2e_shorah_with_extended_window_mode():
+    cwd_test_e2e_extended_window_mode = "./data_1/test_e2e_extended_window_modee"
+    # Check if the directory exists, if not, create it
+    if not os.path.exists(cwd_test_e2e_shorah_with_extended_window_mode):
+        os.makedirs(cwd_test_e2e_shorah_with_extended_window_mode)
     p = subprocess.run(
-        "./shotgun_test.sh --extended_window_mode", shell=True, check=True, cwd=cwd
+        "../shotgun_test.sh --extended_window_mode", shell=True, check=True, cwd=cwd_test_e2e_extended_window_mode
     )
 
     assert p.returncode == 0
-    assert os.path.isfile(os.path.join(cwd, f_path)) == True
+    assert os.path.isfile(os.path.join(cwd_test_e2e_extended_window_mode, f_path)) == True