Resolve "process_getRef"

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  Closes #29 (closed)

/cc @ghenry @venkat.malladi

workflow/tests/test_alignReads.py

@@ -7,8 +7,6 @@ import utils
 
 data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 	'/../../'
-logs_output_path = os.path.dirname(os.path.abspath(__file__)) + \
-	'/../../'
 
 
 @pytest.mark.alignData
@@ -27,15 +25,15 @@ def test_alignData_pe():
 
 @pytest.mark.alignLogs
 def test_alignLogs_se():
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.err'))
-	assert '34497376 reads; of these:' in open(os.path.join(logs_output_path, '16-1ZX4.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, '16-1ZX4.align.out'))
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.err'))
+	assert '34497376 reads; of these:' in open(os.path.join(data_output_path, '16-1ZX4.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(data_output_path, '16-1ZX4.align.out'))
 
 
 @pytest.mark.alignLogs
 def test_alignLogs_pe():
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.err'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.err')) == 7
-	assert '15824858 reads; of these:' in open(os.path.join(logs_output_path, 'Q-Y5JA.align.err')).readlines()[0]
-	assert os.path.exists(os.path.join(logs_output_path, 'Q-Y5JA.align.out'))
-	assert utils.count_lines(os.path.join(logs_output_path, 'Q-Y5JA.align.out')) == 0
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.err'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.err')) == 7
+	assert '15824858 reads; of these:' in open(os.path.join(data_output_path, 'Q-Y5JA.align.err')).readlines()[0]
+	assert os.path.exists(os.path.join(data_output_path, 'Q-Y5JA.align.out'))
+	assert utils.count_lines(os.path.join(data_output_path, 'Q-Y5JA.align.out')) == 0