From 82a4e5a5779e7429c84318926766559ddfd70cc1 Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Tue, 12 Mar 2019 14:06:35 -0500
Subject: [PATCH] Fix tests.
---
.gitlab-ci.yml | 4 ++--
workflow/tests/test_diff_peaks.py | 9 ++++-----
2 files changed, 6 insertions(+), 7 deletions(-)
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 32a376d..fa19e08 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -48,7 +48,7 @@ single_end_diff:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
- - pytest -m singlediff singlediff_true
+ - pytest -m singlediff
artifacts:
expire_in: 2 days
@@ -72,6 +72,6 @@ single_end_skip:
- master
script:
- nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true -resume
- - pytest -m singlediff singleskip_true
+ - pytest -m singleskip_true
artifacts:
expire_in: 2 days
diff --git a/workflow/tests/test_diff_peaks.py b/workflow/tests/test_diff_peaks.py
index 29868ee..8782f21 100644
--- a/workflow/tests/test_diff_peaks.py
+++ b/workflow/tests/test_diff_peaks.py
@@ -10,7 +10,6 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
'/../output/diffPeaks/'
-@pytest.mark.singleend
@pytest.mark.singleskip_true
def test_diff_peaks_singleend_single_rep():
assert os.path.isdir(test_output_path) == False
@@ -21,22 +20,22 @@ def test_diff_peaks_pairedend_single_rep():
assert os.path.isdir(test_output_path) == False
-@pytest.mark.singlediff_true
+@pytest.mark.singlediff
def test_heatmap_singleend_multiple_rep():
assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
-@pytest.mark.singlediff_true
+@pytest.mark.singlediff
def test_pca_singleend_multiple_rep():
assert os.path.exists(os.path.join(test_output_path, 'pca.pdf'))
-@pytest.mark.singlediff_true
+@pytest.mark.singlediff
def test_normcount_singleend_multiple_rep():
assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt'))
-@pytest.mark.singlediff_true
+@pytest.mark.singlediff
def test_diffbind_singleend_multiple_rep():
if os.path.isfile(os.path.join(test_output_path, 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.bed')):
assert os.path.exists(os.path.join(test_output_path, 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.bed'))
--
GitLab