From 947e75436a835dd1bafc3f17ecaa3993c77467f6 Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Wed, 15 Jan 2020 14:26:52 -0600
Subject: [PATCH] Combine trimData CI se/pe into 1 unit test
---
.gitlab-ci.yml | 10 ++--------
workflow/tests/test_trimData.py | 7 ++-----
2 files changed, 4 insertions(+), 13 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index db8d6ca..f35caee 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -26,19 +26,13 @@ getData:
- singularity run 'docker://bicf/gudmaprbkfilexfer:1.3' sh ./workflow/scripts/bdbagFetch.sh Replicate_16-1ZX4 16-1ZX4
- pytest -m getData
-trimData_se:
+trimData:
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
- - pytest -m trimData_pe
+ - pytest -m trimData
integration_se:
stage: integration
diff --git a/workflow/tests/test_trimData.py b/workflow/tests/test_trimData.py
index 8fda067..ea75252 100644
--- a/workflow/tests/test_trimData.py
+++ b/workflow/tests/test_trimData.py
@@ -8,11 +8,8 @@ import os
test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../../'
-@pytest.mark.trimData_se
-def test_trimData_se():
+@pytest.mark.trimData
+def test_trimData():
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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