Add CI for fastqc

.gitlab-ci.yml

@@ -67,6 +67,12 @@ dedupData:
   - singularity exec 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=./test_data/bam/small/Q-Y5JA_1M.se.sorted.bam O=Q-Y5JA_1M.se.deduped.bam M=Q-Y5JA_1M.se.deduped.Metrics.txt REMOVE_DUPLICATES=true
   - pytest -m dedupData
 
+fastqc:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/fastqc:2.0.0' ./test_data/fastq/small/Q-Y5JA_1M.R1.fastq.gz
+  - pytest -m fastqc
+
 integration_se:
   stage: integration
   script:

workflow/tests/test_fastqc.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.fastqc
+def test_trimData_se():
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_1M.R1_fastqc.zip'))
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