From a28ab7897197a7a13e7fe87dbcdb42acb1592855 Mon Sep 17 00:00:00 2001
From: s181706 <jonathan.gesell@utsouthwestern.edu>
Date: Thu, 30 Jan 2020 10:24:46 -0600
Subject: [PATCH] Added unit testing
---
.gitlab-ci.yml | 6 ++++++
workflow/tests/test_dedupReads.py | 33 +++++++++++++++++++++++++++++++
2 files changed, 39 insertions(+)
create mode 100644 workflow/tests/test_dedupReads.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 6ea53a7..d6f9e17 100644
--- a/.gitlab-ci.yml
+++ b/.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:
diff --git a/workflow/tests/test_dedupReads.py b/workflow/tests/test_dedupReads.py
new file mode 100644
index 0000000..a2d7e5e
--- /dev/null
+++ b/workflow/tests/test_dedupReads.py
@@ -0,0 +1,33 @@
+#!/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'))
--
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