Check differential peaks.

.gitlab-ci.yml

@@ -35,7 +35,7 @@ single_end_diff:
   stage: integration
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
-  - pytest -m pairedend
+  - pytest -m singlediff
   - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days
@@ -44,7 +44,7 @@ paired_end_diff:
   stage: integration
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
-  - pytest -m pairedend
+  - pytest -m paireddiff
   - pytest --cov=./workflow/scripts
   artifacts:
     expire_in: 2 days

workflow/tests/test_diff_peaks.py

+#!/usr/bin/env python3
+
+import pytest
+import pandas as pd
+from io import StringIO
+import os
+import utils
+
+test_output_path = os.path.dirname(os.path.abspath(__file__)) + \
+                '/../output/diffPeaks/'
+
+
+@pytest.mark.singleend
+def test_diff_peaks_singleend_single_rep():
+    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
+
+
+@pytest.mark.pairedend
+def test_annotate_peaks_pairedend_single_rep():
+    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.bed'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_diffbind.csv'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_heatmap.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'no_pca.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.pdf'))
+
+@pytest.mark.singlediff
+def test_diff_peaks_singleend_multiple_rep():
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'pca.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.bed'))
+    diffbind_file = test_output_path + 'ENCSR272GNQ_vs_ENCSR238SGC_diffbind.csv'
+    assert os.path.exists(diffbind_file)
+    assert utils.count_lines(diffbind_file) == 201039
+
+@pytest.mark.paireddiff
+def test_annotate_peaks_pairedend_single_rep():
+    assert os.path.exists(os.path.join(test_output_path, 'heatmap.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'pca.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'normcount_peaksets.txt'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR729LGA_vs_ENCSR757EMK_diffbind.bed'))
+    diffbind_file = test_output_path + 'ENCSR729LGA_vs_ENCSR757EMK_diffbind.csv'
+    assert os.path.exists(diffbind_file)
+    assert utils.count_lines(diffbind_file) == 112652