From 8f580cc724e4104c5a18db2d0c041af1a2eeaa46 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Mon, 3 Feb 2020 21:57:59 -0600
Subject: [PATCH] Add CI for fastqc

---
 .gitlab-ci.yml                |  6 ++++++
 workflow/tests/test_fastqc.py | 13 +++++++++++++
 2 files changed, 19 insertions(+)
 create mode 100644 workflow/tests/test_fastqc.py

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 37083c1..41afb3f 100644
--- a/.gitlab-ci.yml
+++ b/.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:
diff --git a/workflow/tests/test_fastqc.py b/workflow/tests/test_fastqc.py
new file mode 100644
index 0000000..6b79d97
--- /dev/null
+++ b/workflow/tests/test_fastqc.py
@@ -0,0 +1,13 @@
+#!/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'))
\ No newline at end of file
-- 
GitLab