Add unit test for outputBag

.gitlab-ci.yml

@@ -130,6 +130,13 @@ dataQC:
     echo "tin.py -i ./test_data/bam/small/Q-Y5F6_1M.se.sorted.deduped.${i}.bam -r /project/BICF/BICF_Core/shared/gudmap/references/GRCh38.p12.v31/bed/genome.bed; cat Q-Y5F6_1M.se.sorted.deduped.${i}.tin.xls | tr -s \"\\w\" \"\\t\" | grep -P \"\\t${i}\\t\";"; done | singularity run 'docker://bicf/rseqc3.0:2.0.1_indev' parallel -j 20 -k >> Q-Y5F6_1M.se.sorted.deduped.tin.xls
   - pytest -m dataQC
 
+outputBag:
+  stage: unit
+  script:
+  - mkdir test
+  - singularity run 'docker://bicf/gudmaprbkfilexfer:2.0.1_indev' bdbag test --archiver zip
+  - pytest -m outputBag
+
 
 integration_se:
   stage: integration
@@ -181,5 +188,4 @@ consistency:
       - assignedPE.txt
       - assignedExpectSE.txt
       - assignedExpectPE.txt
-    expire_in: 7 days
-
+    expire_in: 7 days
\ No newline at end of file

workflow/tests/test_outputBag.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.outputBag
+def test_outputBag():
+    assert os.path.exists(os.path.join(test_output_path, 'test.zip'))