diff --git a/tests/__init__.py b/tests/__init__.py
new file mode 100644
index 0000000..c2443ab
--- /dev/null
+++ b/tests/__init__.py
@@ -0,0 +1,51 @@
+import unittest
+import os
+
+
+class TestSConsPipelineOutput(unittest.TestCase):
+    def test_pipeline_output(self):
+        output_dir = 'test_output'
+
+        output_files = [
+            'blast',
+            'lineages.csv',
+            'seqs.fasta',
+            'seq_info.csv',
+            'taxonomy.csv',
+            ]
+
+        expected = {}
+        for date_dir in os.listdir(output_dir):
+            if len(date_dir) == 8 and date_dir.isnumeric():
+                out = f'{output_dir}/{date_dir}'
+                self.assertTrue(os.path.isfile(out + '/SUCCESS'))
+                expected.update({
+                    f'{out}/dedup/1200bp/types': output_files,
+                    f'{out}/dedup/1200bp/named/': output_files,
+                    f'{out}/dedup/1200bp/named/filtered': [
+                        'blast',
+                        'taxonomy.csv',
+                        'outliers.csv',
+                        'unsorted.fasta'],
+                    f'{out}/dedup/1200bp/named/filtered/trusted': output_files,
+                    f'{out}/dedup/1200bp/named/filtered/types': output_files,
+                    })
+
+        # Verify the folder structure and contents
+        for folder_path, contents in expected.items():
+            self.assertTrue(
+                os.path.isdir(folder_path),
+                f"Folder {folder_path} does not exist")
+            actual_contents = os.listdir(folder_path)
+            for expected_file in contents:
+                self.assertIn(
+                    expected_file,
+                    actual_contents,
+                    f"{expected_file} not found in {folder_path}")
+                file = os.path.join(folder_path, expected_file)
+                self.assertTrue(os.path.isfile(file))
+                self.assertTrue(os.stat(file).st_size > 0)  # not empty
+
+
+if __name__ == '__main__':
+    unittest.main()