diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index add0a9b8765623c74e59deadf180e2739c2a7da7..f92dcb4d2c51caf363e3798ac1c9046793f5b79e 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -50,6 +50,12 @@ trimData:
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA_1M.pe -j `nproc` ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz ./test_data/fastq/small/Q-Y5JA_1M.R2.fastq.gz
   - pytest -m trimData
 
+downsampleData:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/seqtk:2.0.0' seqtk sample -s100 ./test_data/fastq/small/Q-Y5JA_1M_trimmed.fq.gz 1000 1> sampled.1.fq
+  - pytest -m downsampleData
+
 alignData:
   stage: unit
   script:
diff --git a/workflow/tests/test_downsampleData.py b/workflow/tests/test_downsampleData.py
new file mode 100644
index 0000000000000000000000000000000000000000..fd42c49e169e387dd9662903b20866c40aec8907
--- /dev/null
+++ b/workflow/tests/test_downsampleData.py
@@ -0,0 +1,13 @@
+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../../'
+
+@pytest.mark.downsampleData
+def test_downsampleData():
+    assert os.path.exists(os.path.join(test_output_path, 'sampled.1.fq'))
\ No newline at end of file