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