Add in paried-end reads test for alignment.

workflow/tests/test_map_reads.py

@@ -18,5 +18,9 @@ def test_map_reads_singleend():
 
 @pytest.mark.integration
 def test_map_reads_pairedend():
-    # Do the same thing for paired end data
-    pass
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam'))
+    aligned_reads_report = test_output_path + 'NCFF002DTU_val_1ENCFF002EFI_val_2.srt.bam.flagstat.qc'
+    samtools_report = open(aligned_reads_report).readlines()
+    assert '72660890 + 0 in total' in samtools_report[0]
+    assert '72053925 + 0 mapped (99.16% : N/A)' in samtools_report[4]
+    assert '71501126 + 0 properly paired (98.40% : N/A)' in samtools_report[8]