Modify tests.

workflow/tests/test_annotate_peaks.py

@@ -16,7 +16,7 @@ def test_annotate_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR238SGC.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 152840
+    assert utils.count_lines(annotation_file) == 149820
 
 
 @pytest.mark.pairedend
@@ -25,4 +25,4 @@ def test_annotate_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.chipseeker_upsetplot.pdf'))
     annotation_file = test_output_path + 'ENCSR729LGA.chipseeker_annotation.tsv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 25391
+    assert utils.count_lines(annotation_file) == 25579

workflow/tests/test_call_peaks_macs.py

@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 def test_call_peaks_macs_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.fc_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.pvalue_signal.bw'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT.xls'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT_peaks.xls'))
     peak_file = test_output_path + 'ENCLB144FDT.narrowPeak'
     assert utils.count_lines(peak_file) == 227389
 
@@ -21,6 +21,6 @@ def test_call_peaks_macs_singleend():
 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'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX_peak.xls'))
     peak_file = test_output_path + 'ENCLB568IYX.narrowPeak'
-    assert utils.count_lines(peak_file) == 112652
+    assert utils.count_lines(peak_file) == 113821

workflow/tests/test_map_qc.py

@@ -31,8 +31,8 @@ def test_map_qc_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.dedup.qc'))
     filtered_reads_report = test_output_path + 'ENCLB568IYX.dedup.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]
+    assert '47388510 + 0 in total' in samtools_report[0]
+    assert '47388510 + 0 mapped (100.00%:N/A)' in samtools_report[4]
     library_complexity = test_output_path + 'ENCLB568IYX.pbc.qc'
     df_library_complexity = pd.read_csv(library_complexity, sep='\t')
     assert  df_library_complexity["NRF"].iloc[0] == 0.947064

workflow/tests/test_overlap_peaks.py

@@ -37,11 +37,11 @@ def test_check_update_design(design_diff):
 def test_overlap_peaks_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR238SGC.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 152848
+    assert utils.count_lines(peak_file) == 149828
 
 
 @pytest.mark.pairedend
 def test_overlap_peaks_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.rejected.narrowPeak'))
     peak_file = test_output_path + 'ENCSR729LGA.replicated.narrowPeak'
-    assert utils.count_lines(peak_file) == 25655
+    assert utils.count_lines(peak_file) == 25847

workflow/tests/test_trim_reads.py

@@ -13,7 +13,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 @pytest.mark.singleend
 def test_trim_reads_singleend():
     raw_fastq = test_data_path + 'ENCFF833BLU.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCLB144FDT_R1.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB144FDT_R1_trimmed.fq.gz'
     trimmed_fastq_report = test_output_path + \
                             'ENCLB144FDT_R1_trimmed.fq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
@@ -24,9 +24,9 @@ def test_trim_reads_singleend():
 @pytest.mark.pairedend
 def test_trim_reads_pairedend():
     raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCLB637LZP_R2.fq.gz'
+    trimmed_fastq = test_output_path + 'ENCLB637LZP_R2_val_2.fq.gz'
     trimmed_fastq_report = test_output_path + \
-                            'ENCLB637LZP_R2_val_2.fq.gz_trimming_report.txt'
+                            'ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2229312710
     assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]

workflow/tests/test_xcor.py

@@ -23,6 +23,6 @@ def test_cross_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.cc.plot.pdf'))
     qc_file = os.path.join(test_output_path,"ENCLB568IYX.cc.qc")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
-    assert df_xcor[2].iloc[0] == '210,220,475'
-    assert round(df_xcor[8].iloc[0],6) == 1.062032
-    assert df_xcor[9].iloc[0] == 3.737722
+    assert df_xcor[2].iloc[0] == '220,430,475'
+    assert round(df_xcor[8].iloc[0],6) == 1.060018
+    assert df_xcor[9].iloc[0] == 4.099357