Add pytest for trim

.gitlab-ci.yml

@@ -22,15 +22,18 @@ getData:
   - ln -sfn `readlink -e ./test_data/auth/cookies.txt` ~/.bdbag/deriva-cookies.txt
   - unzip ./test_data/bagit/Replicate_16-1ZX4
   - singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
+  - pytest -m getData
 
 trimData_se:
   stage: unit
   script:
   - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
   - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --basename 16-1ZX4 -j ${ncore} ./test_data/fastq/16-1ZX4.R1.fastq.gz
+  - pytest -m trimData_se
 
 trimData_pe:
   stage: unit
   script:
   - if [ `nproc` -gt 8 ]; then ncore=8; else ncore=`nproc`; fi
-  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
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+  - singularity run 'docker://bicf/trimgalore:1.1' trim_galore --gzip -q 25 --illumina --length 35 --paired --basename Q-Y5JA -j ${ncore} ./test_data/fastq/Q-Y5JA.R1.fastq.gz ./test_data/fastq/Q-Y5JA.R2.fastq.gz
+  - pytest -m trimData_pe
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workflow/tests/test_trimData.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.trimData_se
+def test_trimData_se():
+    assert os.path.exists(os.path.join(test_output_path, '16-1ZX4_trimmed.fq.gz'))
+
+@pytest.mark.trimData_pe
+def test_trimData_pe():
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R1_val_1.fq.gz'))
+    assert os.path.exists(os.path.join(test_output_path, 'Q-Y5JA_R2_val_2.fq.gz'))
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