Added unit testing

.gitlab-ci.yml

@@ -55,6 +55,12 @@ alignReads:
   - singularity run 'docker://bicf/gudmaprbkaligner:2.0.0' samtools index -@ `nproc` -b 16-1ZX4.sorted.bam 16-1ZX4.sorted.bai
   - pytest -m alignData
 
+dedupReads:
+  stage: unit
+  script:
+  - singularity run 'docker://bicf/picard2.21.7:2.0.0' java -jar /picard/build/libs/picard.jar MarkDuplicates I=${sortedBam} O=${repRID}.deduped.bam M=${repRID}.deduped.Metrics.txt REMOVE_DUPLICATES=true
+  - pytest -m dedupData
+
 integration_se:
   stage: integration
   script:

workflow/tests/test_dedupReads.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+import os
+import utils
+
+data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../'
+logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+	'/../../'
+
+
+@pytest.mark.dedupData
+def test_dedupData_se():
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.deduped.bm'))
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.deduped.Metrics.txt'))
+
+@pytest.mark.dedupData
+def test_dedupData_pe():
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.deduped.bm'))
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.deduped.Metrics.txt'))
+
+
+@pytest.mark.dedupLogs
+def test_dedupLogs_se():
+	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.dedup.err'))
+	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.dedup.out'))
+
+@pytest.mark.dedupLogs
+def test_dedupLogs_pe():
+	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.dedup.err'))
+	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.dedup.out'))