Add in paired-end filter test.

workflow/tests/test_map_qc.py

@@ -25,5 +25,14 @@ def test_map_qc_singleend():
 
 @pytest.mark.integration
 def test_map_qc_pairedend():
-    # Do the same thing for paired end data
-    pass
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bambai'))
+    filtered_reads_report = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.flagstat.qc'
+    samtools_report = open(filtered_reads_report).readlines()
+    assert '47389080 + 0 in total' in samtools_report[0]
+    assert '47389080 + 0 mapped (100.00%:N/A)' in samtools_report[4]
+    library_complexity = test_output_path + 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.pbc.qc'
+    df_library_complexity = pd.read_csv(library_complexity, sep='\t')
+    assert  df_library_complexity["NRF"].iloc[0] == 0.947064
+    assert  df_library_complexity["PBC1"].iloc[0] == 0.946724
+    assert  df_library_complexity["PBC2"].iloc[0] == 18.643039