Update paths and add in testing if file exists.

workflow/tests/test_map_reads.py

@@ -3,10 +3,13 @@
 import pytest
 import os
 
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/alignReads/'
+
 
 def test_map_reads_singleend():
-    aligned_reads_report = os.path.dirname(os.path.abspath(__file__)) + \
-                '/../output/alignReads/ENCFF646LXU.srt.bam.flagstat.qc'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF646LXU.srt.bam'))
+    aligned_reads_report = test_output_path + 'ENCFF646LXU.srt.bam.flagstat.qc'
     samtools_report = open(aligned_reads_report).readlines()
     assert '80795025 + 0 in total' in samtools_report[0]
     assert '80050072 + 0 mapped (99.08% : N/A)' in samtools_report[4]