Commit ee0828f0 authored by Venkat Malladi's avatar Venkat Malladi
Browse files

Update tests and add a skip test that only runs on branches.

parent aa5566a2
Pipeline #3178 canceled with stages
in 40 seconds
......@@ -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
......@@ -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'
......
......@@ -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'))
......
......@@ -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'))
......
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