workflow/tests/test_motif_search.py

@@ -10,18 +10,32 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
                 '/../output/motifSearch/'
 
 
+@pytest.mark.singleend
+def test_limited_peaks_singleend():
+    peak_file_ENCSR238SGC = test_output_path + 'ENCSR238SGC.600.narrowPeak'
+    assert os.path.exists(peak_file_ENCSR238SGC)
+    assert utils.count_lines(peak_file_ENCSR238SGC) == 600
+
+
 @pytest.mark.singleend
 def test_motif_search_singleend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'ENCSR238SGC.fa'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC_memechip', 'index.html'))
-    peak_file_ENCSR238SGC = test_output_path + 'sorted-ENCSR238SGC.replicated.narrowPeak'
-    assert os.path.exists(peak_file_ENCSR238SGC)
-    assert utils.count_lines(peak_file_ENCSR238SGC) == 600
+
+
+@pytest.mark.singleskip_true
+def test_motif_search_singleend():
+    assert os.path.isdir(test_output_path) == False
+
+
+@pytest.mark.pairedend
+def test_limited_peaks_pairedend():
+    peak_file_ENCSR729LGA= test_output_path + 'ENCSR729LGA.600.narrowPeak'
+    assert os.path.exists(peak_file_ENCSR729LGA)
+    assert utils.count_lines(peak_file_ENCSR729LGA) == 600
+
 
 @pytest.mark.pairedend
 def test_motif_search_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip',  'ENCSR729LGA.fa'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_memechip', 'index.html'))
-    peak_file_ENCSR729LGA= test_output_path + 'sorted-ENCSR729LGA.replicated.narrowPeak'
-    assert os.path.exists(peak_file_ENCSR729LGA)
-    assert utils.count_lines(peak_file_ENCSR729LGA) == 600

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) == 152262
 
 
 @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) == 25758

workflow/tests/test_trim_reads.py

@@ -13,20 +13,28 @@ 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 + 'ENCFF833BLU_trimmed.fq.gz'
-    trimmed_fastq_report = test_output_path + \
-                            'ENCFF833BLU.fastq.gz_trimming_report.txt'
+    trimmed_fastq = test_output_path + 'ENCLB144FDT/ENCLB144FDT_R1_trimmed.fq.gz'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2512853101
+
+
+@pytest.mark.singleend
+def test_trim_report_singleend():
+    trimmed_fastq_report = test_output_path + \
+                            'ENCLB144FDT/ENCLB144FDT_R1.fastq.gz_trimming_report.txt'
     assert 'Trimming mode: single-end' in open(trimmed_fastq_report).readlines()[4]
 
 
 @pytest.mark.pairedend
 def test_trim_reads_pairedend():
     raw_fastq = test_data_path + 'ENCFF582IOZ.fastq.gz'
-    trimmed_fastq = test_output_path + 'ENCFF582IOZ_val_2.fq.gz'
-    trimmed_fastq_report = test_output_path + \
-                            'ENCFF582IOZ.fastq.gz_trimming_report.txt'
+    trimmed_fastq = test_output_path + 'ENCLB637LZP/ENCLB637LZP_R2_val_2.fq.gz'
     assert os.path.getsize(raw_fastq) != os.path.getsize(trimmed_fastq)
     assert os.path.getsize(trimmed_fastq) == 2229312710
+
+
+@pytest.mark.pairedend
+def test_trim_report_pairedend():
+    trimmed_fastq_report = test_output_path + \
+                            'ENCLB637LZP/ENCLB637LZP_R2.fastq.gz_trimming_report.txt'
     assert 'Trimming mode: paired-end' in open(trimmed_fastq_report).readlines()[4]

workflow/tests/test_xcor.py

@@ -9,9 +9,13 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 
 @pytest.mark.singleend
-def test_cross_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
-    qc_file = os.path.join(test_output_path,"ENCFF833BLU.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
+def test_cross_plot_singleend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB144FDT/ENCLB144FDT.cc.plot.pdf'))
+
+
+@pytest.mark.singleend
+def test_cross_qc_singleend():
+    qc_file = os.path.join(test_output_path,"ENCLB144FDT/ENCLB144FDT.cc.qc")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
     assert df_xcor[2].iloc[0] == '190,200,210'
     assert df_xcor[8].iloc[0] == 1.025906
@@ -19,10 +23,14 @@ def test_cross_singleend():
 
 
 @pytest.mark.pairedend
-def test_cross_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.plot.pdf'))
-    qc_file = os.path.join(test_output_path,"ENCFF582IOZ_val_2ENCFF957SQS_val_1.filt.nodup.tagAlign.15.tagAlign.gz.cc.qc")
+def test_cross_qc_pairedend():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX/ENCLB568IYX.cc.plot.pdf'))
+
+
+@pytest.mark.pairedend
+def test_cross_plot_pairedend():
+    qc_file = os.path.join(test_output_path,"ENCLB568IYX/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