Fix the actual tests

workflow/tests/test_alignReads.py

@@ -10,23 +10,25 @@ data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 	'/../../'
 
+
 @pytest.mark.alignData
 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')) == 5805611
+	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')) == 12824
+	assert utils.count_lines(os.path.join(data_output_path, '16-1ZX4.sorted.bai')) == 13112
+
 
 @pytest.mark.alignData
 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')) == 4246125
+	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')) == 12824
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.sorted.bai')) == 10415
 
 
 @pytest.mark.alignLogs
@@ -37,6 +39,7 @@ def test_alignLogs_se():
 	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
 	assert utils.count_lines(os.path.join(logs_output_path, '16-1ZX4.align.out')) == 0
 
+
 @pytest.mark.alignLogs
 def test_alignLogs_pe():
 	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))