From ee0828f0b15d6977719c95b7b0b5610c2a7a2b97 Mon Sep 17 00:00:00 2001 From: Venkat Malladi <venkat.malladi@utsouthwestern.edu> Date: Sat, 9 Mar 2019 22:03:16 -0600 Subject: [PATCH] Update tests and add a skip test that only runs on branches. --- .gitlab-ci.yml | 15 ++++++++++++++- workflow/tests/test_annotate_peaks.py | 1 + workflow/tests/test_diff_peaks.py | 11 +++++++---- workflow/tests/test_motif_search.py | 7 ++++++- 4 files changed, 28 insertions(+), 6 deletions(-) diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml index 6d2c02b..e5ff36c 100644 --- a/.gitlab-ci.yml +++ b/.gitlab-ci.yml @@ -8,6 +8,7 @@ stages: - unit - single - multiple + - skip user_configuration: stage: unit @@ -47,7 +48,7 @@ single_end_diff: - master script: - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume - - pytest -m singlediff + - pytest -m singlediff singlediff_true artifacts: expire_in: 2 days @@ -62,3 +63,15 @@ paired_end_diff: - pytest -m paireddiff artifacts: expire_in: 2 days + +single_end_skip: + stage: multiple + only: + - branches + except: + - master + script: + - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --skipDiff true --skipMotif true -resume + - pytest -m singlediff singleskip_true + artifacts: + expire_in: 2 days diff --git a/workflow/tests/test_annotate_peaks.py b/workflow/tests/test_annotate_peaks.py index ee3ebe1..1342a12 100644 --- a/workflow/tests/test_annotate_peaks.py +++ b/workflow/tests/test_annotate_peaks.py @@ -19,6 +19,7 @@ def test_pie_singleend(): def test_upsetplot_singleend(): assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf')) + @pytest.mark.singleend def test_annotation_singleend(): annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv' diff --git a/workflow/tests/test_diff_peaks.py b/workflow/tests/test_diff_peaks.py index b0a76aa..29868ee 100644 --- a/workflow/tests/test_diff_peaks.py +++ b/workflow/tests/test_diff_peaks.py @@ -11,29 +11,32 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \ @pytest.mark.singleend +@pytest.mark.singleskip_true def test_diff_peaks_singleend_single_rep(): assert os.path.isdir(test_output_path) == False + @pytest.mark.pairedend def test_diff_peaks_pairedend_single_rep(): assert os.path.isdir(test_output_path) == False -@pytest.mark.singlediff + +@pytest.mark.singlediff_true def test_heatmap_singleend_multiple_rep(): assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf')) -@pytest.mark.singlediff +@pytest.mark.singlediff_true def test_pca_singleend_multiple_rep(): assert os.path.exists(os.path.join(test_output_path, 'pca.pdf')) -@pytest.mark.singlediff +@pytest.mark.singlediff_true def test_normcount_singleend_multiple_rep(): assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt')) -@pytest.mark.singlediff +@pytest.mark.singlediff_true 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')) diff --git a/workflow/tests/test_motif_search.py b/workflow/tests/test_motif_search.py index 8c12652..28aec04 100644 --- a/workflow/tests/test_motif_search.py +++ b/workflow/tests/test_motif_search.py @@ -23,13 +23,18 @@ def test_motif_search_singleend(): assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html')) +@pytest.mark.singleskip_true +def test_motif_search_singleend(): + assert os.path.isdir(test_output_path) == False + + @pytest.mark.pairedend def test_limited_peaks_pairedend(): peak_file_ENCSR729LGA= test_output_path + 'ENCSR729LGA.600.narrowPeak' assert os.path.exists(peak_file_ENCSR729LGA) assert utils.count_lines(peak_file_ENCSR729LGA) == 600 - + @pytest.mark.pairedend def test_motif_search_pairedend(): assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'ENCSR729LGA.fa')) -- GitLab