From c7ea5cbafb2401c786621ca00d66c021a4f56474 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Tue, 14 Jan 2020 14:16:08 -0600
Subject: [PATCH] Add pytest for trim
---
.gitlab-ci.yml | 5 ++++-
workflow/tests/test_trimData.py | 18 ++++++++++++++++++
2 files changed, 22 insertions(+), 1 deletion(-)
create mode 100644 workflow/tests/test_trimData.py
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 8491804..a83427a 100644
--- a/.gitlab-ci.yml
+++ b/.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
\ No newline at end of file
+ - 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
\ No newline at end of file
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
new file mode 100644
index 0000000..8fda067
--- /dev/null
+++ b/workflow/tests/test_trimData.py
@@ -0,0 +1,18 @@
+#!/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'))
\ No newline at end of file
--
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