Fixed test data and test output.

test_data/design_diff_PE.txt

@@ -4,4 +4,4 @@ ENCLB568IYX	ENCSR729LGA	MCF-7	SP1	None	2	ENCLB336TVW	ENCFF330MCZ.fastq.gz	ENCFF2
 ENCLB678IDC	ENCSR217LRF	MCF-7	Control	None	1	ENCLB678IDC	ENCFF002DTU.fastq.gz	ENCFF002EFI.fastq.gz
 ENCLB336TVW	ENCSR217LRF	MCF-7	Control	None	2	ENCLB336TVW	ENCFF002EFG.fastq.gz	ENCFF002DTS.fastq.gz
 ENCLB552ACZ	ENCSR757EMK	MCF-7	SUZ12	None	1	ENCLB678IDC	ENCFF833EZX.fastq.gz	ENCFF161HBP.fastq.gz
-ENCLB568IYX	ENCSR757EMK	MCF-7	SUZ12	None	2	ENCLB336TVW	ENCFF776KZU.fastq.gz	ENCFF119KHM.fastq.gz
+ENCLB872TQR	ENCSR757EMK	MCF-7	SUZ12	None	2	ENCLB336TVW	ENCFF776KZU.fastq.gz	ENCFF119KHM.fastq.gz

workflow/tests/test_annotate_peaks.py

@@ -21,8 +21,8 @@ def test_annotate_peaks_singleend():
 
 @pytest.mark.pairedend
 def test_annotate_peaks_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LGA.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LGA.chipseeker_upsetplot.pdf'))
-    annotation_file = test_output_path + 'ENCSR217LGA.chipseeker_annotation.csv'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_pie.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA..chipseeker_upsetplot.pdf'))
+    annotation_file = test_output_path + 'ENCSR729LGA..chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
     assert utils.count_lines(annotation_file) == 25391

workflow/tests/test_call_peaks_macs.py

@@ -21,4 +21,4 @@ def test_call_peaks_macs_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
     peak_file = test_output_path + 'ENCLB568IYX_peaks.narrowPeak'
-    assert utils.count_lines(peak_file) == 138827
+    assert utils.count_lines(peak_file) == 112652