Merge branch 'develop' into 'master'

Develop

See merge request !68

workflow/tests/test_makeFeatureCounts.py

@@ -5,15 +5,15 @@ import pandas as pd
 import os
 import utils
 
-data_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
     '/../../'
 
 
 @pytest.mark.makeFeatureCounts
 def test_makeFeatureCounts():
     assert os.path.exists(os.path.join(
-        data_output_path, 'Q-Y5F6_1M.se_countData'))
+        test_output_path, 'Q-Y5F6_1M.se_countData'))
     assert os.path.exists(os.path.join(
-        data_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
+        test_output_path, 'Q-Y5F6_1M.se.countTable.csv'))
     assert os.path.exists(os.path.join(
-        data_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))
+        test_output_path, 'Q-Y5F6_1M.se_tpmTable.csv'))

workflow/tests/test_parseMetadata.py

@@ -19,7 +19,7 @@ def readLine(fileName):
     data = False
     file = open(fileName, "r")
     line = file.readline()
-    if line.strip() == "uk,uk,se,unstranded,no,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
+    if line.strip() == "uk,uk,se,unstranded,f,Homo sapiens,75,Experiment_RID,Study_RID,Replicate_RID":
         data = True
 
     return data