Test data for single control single replicate.

.gitlab-ci.yml

@@ -14,7 +14,6 @@ stages:
 user_configuration:
   stage: unit
   script:
-  - pytest -m unit
   - pytest -m unit --cov=./workflow/scripts
 
 astrocyte:
@@ -51,7 +50,8 @@ single_end_single_control:
     - master
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_single_contol_SE.txt" --genome 'GRCh38' --pairedEnd false --astrocyte false
-
+  - pytest -m singlecontrol
+  
 single_end_diff:
   stage: multiple
   only:

test_data/design_single_contol_SE.txt

 sample_id	experiment_id	biosample	factor	treatment	replicate	control_id	fastq_read1
 ENCLB497XZB	ENCSR000DXB	Panc1	H3K4me3	None	1	ENCLB304SBJ	ENCFF001GBW.fastq.gz
-ENCLB414AAH	ENCSR000DXB	Panc1	H3K4me3	None	2	ENCLB304SBJ	ENCFF001GBV.fastq.gz
 ENCLB304SBJ	ENCSR000DXC	Panc1	Control	None	1	ENCLB304SBJ	ENCFF001HWJ.fastq.gz

workflow/tests/test_overlap_peaks.py

@@ -45,3 +45,9 @@ 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) >= 25657
+
+@pytest.mark.singlecontrol
+def test_overlap_peaks_singlecontrol():
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR000DXB.rejected.narrowPeak'))
+    peak_file = test_output_path + 'ENCSR000DXB.replicated.narrowPeak'
+    assert utils.count_lines(peak_file) >= 35097