Add in paired end tests for calling peaks.

.gitlab-ci.yml

@@ -25,6 +25,6 @@ single_end_mouse:
 paired_end_human:
   stage: integration
   script:
-  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
+  - nextflow run workflow/main.nf --designFile "/work/BICF/s163035/builds/932983dd/0/BICF/Astrocyte/chipseq_analysis/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   artifacts:
     expire_in: 2 days

workflow/tests/test_call_peaks_macs.py

@@ -18,5 +18,7 @@ def test_call_peaks_macs_singleend():
 
 @pytest.mark.integration
 def test_call_peaks_macs_pairedend():
-    # Do the same thing for paired end data
-    pass
+    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) == 112652

workflow/tests/test_experiment_design.py

@@ -40,5 +40,7 @@ def test_experiment_design_single_end():
 
 @pytest.mark.integration
 def test_experiment_design_paired_end():
-    # Do the same thing for paired end data
-    pass
+    design_file = os.path.join(test_output_path, 'ENCSR729LGA.tsv')
+    assert os.path.exists(design_file)
+    design_df = pd.read_csv(design_file, sep="\t")
+    assert design_df.shape[0] == 2

workflow/tests/test_pool_and_psuedoreplicate.py

@@ -70,5 +70,7 @@ def test_pool_and_psuedoreplicate_single_end():
 
 @pytest.mark.integration
 def test_experiment_design_paired_end():
-    # Do the same thing for paired end data
-    pass
+    design_file = os.path.join(test_output_path, 'ENCSR729LGA_ppr.tsv')
+    assert os.path.exists(design_file)
+    design_df = pd.read_csv(design_file, sep="\t")
+    assert design_df.shape[0] == 5