Add unit test for downsampleData

.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:

workflow/tests/test_downsampleData.py

+#!/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'))
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