Fix what tests are run and the testing output.

.gitlab-ci.yml

@@ -12,13 +12,13 @@ user_configuration:
   stage: unit
   script:
   - pytest -m unit
+  -pytest -m unit --cov=./workflow/scripts
 
 single_end_mouse:
   stage: integration
   script:
   - nextflow run workflow/main.nf -resume
   - pytest -m singleend
-  - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days
 
@@ -27,7 +27,6 @@ paired_end_human:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   - pytest -m pairedend
-  - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days
 
@@ -36,7 +35,6 @@ single_end_diff:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
   - pytest -m singlediff
-  - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days
 
@@ -45,6 +43,5 @@ paired_end_diff:
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   - pytest -m paireddiff
-  - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days

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.csv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 152840
+    assert utils.count_lines(annotation_file) == 149820
 
 
 @pytest.mark.pairedend

workflow/tests/test_map_qc.py

@@ -26,7 +26,7 @@ def test_map_qc_singleend():
 @pytest.mark.pairedend
 def test_map_qc_pairedend():
     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'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCFF293YFE_val_2ENCFF330MCZ_val_1.filt.nodup.bam.bai'))
     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]

workflow/tests/test_motif_search.py

@@ -12,7 +12,7 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 @pytest.mark.singleend
 def test_motif_search_singleend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR238SGC.fa'))
+    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)
@@ -20,7 +20,7 @@ def test_motif_search_singleend():
 
 @pytest.mark.pairedend
 def test_motif_search_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA.fa'))
+    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)

workflow/tests/test_xcor.py

@@ -9,20 +9,20 @@ test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
 
 
 @pytest.mark.singleend
-def test_map_qc_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")
     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
-    assert df_xcor[9].iloc[0] == 1.139671
+    assert round(df_xcor[9].iloc[0], 6) == 1.139671
 
 
 @pytest.mark.pairedend
-def test_map_qc_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")
     df_xcor = pd.read_csv(qc_file, sep="\t", header=None)
     assert df_xcor[2].iloc[0] == '210,220,475'
-    assert df_xcor[8].iloc[0] == 1.062032
+    assert round(df_xcor[8].iloc[0],6) == 1.062032
     assert df_xcor[9].iloc[0] == 3.737722