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Commit 2333e8b4 authored by Venkat Malladi's avatar Venkat Malladi
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Remove line testing. As count_lines doesn't work for bam and bai files

parent e94986e1
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2 merge requests!37v0.0.1,!15Resolve "process_align"
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workflow/tests/test_alignReads.py
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......@@ -16,9 +16,7 @@ def test_alignData_se():
assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.unal.gz'))
assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.unal.gz')) == 3070528
assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.sorted.bam'))
assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.sorted.bam')) == 3829750
assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.sorted.bai'))
assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.sorted.bai')) == 13112
@pytest.mark.alignData
......@@ -26,9 +24,7 @@ def test_alignData_pe():
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.unal.gz'))
assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.unal.gz')) == 0
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam'))
assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bam')) == 4743572
assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai'))
assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai')) == 10415
@pytest.mark.alignLogs
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