fix merge.

.gitlab-ci.yml

@@ -6,7 +6,8 @@ before_script:
 
 stages:
   - unit
-  - integration
+  - single
+  - multiple
 
 user_configuration:
   stage: unit
@@ -15,7 +16,7 @@ user_configuration:
   -pytest -m unit --cov=./workflow/scripts
 
 single_end_mouse:
-  stage: integration
+  stage: single
   script:
   - nextflow run workflow/main.nf -resume
   - pytest -m singleend
@@ -23,7 +24,7 @@ single_end_mouse:
     expire_in: 2 days
 
 paired_end_human:
-  stage: integration
+  stage: single
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   - pytest -m pairedend
@@ -31,7 +32,7 @@ paired_end_human:
     expire_in: 2 days
 
 single_end_diff:
-  stage: integration
+  stage: multiple
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' -resume
   - pytest -m singlediff
@@ -39,7 +40,7 @@ single_end_diff:
     expire_in: 2 days
 
 paired_end_diff:
-  stage: integration
+  stage: multiple
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_PE.txt" --genome 'GRCh38' --pairedEnd true -resume
   - pytest -m paireddiff

workflow/tests/test_annotate_peaks.py

@@ -21,8 +21,8 @@ def test_annotate_peaks_singleend():
 
 @pytest.mark.pairedend
 def test_annotate_peaks_pairedend():
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_pie.pdf'))
-    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LRF.chipseeker_upsetplot.pdf'))
-    annotation_file = test_output_path + 'ENCSR217LRF.chipseeker_annotation.csv'
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LGA.chipseeker_pie.pdf'))
+    assert os.path.exists(os.path.join(test_output_path, 'ENCSR217LGA.chipseeker_upsetplot.pdf'))
+    annotation_file = test_output_path + 'ENCSR217LGA.chipseeker_annotation.csv'
     assert os.path.exists(annotation_file)
-    assert utils.count_lines(annotation_file) == 25390
+    assert utils.count_lines(annotation_file) == 25391

workflow/tests/test_call_peaks_macs.py

@@ -23,4 +23,4 @@ def test_call_peaks_macs_pairedend():
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.pvalue_signal.bw'))
     assert os.path.exists(os.path.join(test_output_path, 'ENCLB568IYX.xls'))
     peak_file = test_output_path + 'ENCLB568IYX.narrowPeak'
-    assert utils.count_lines(peak_file) == 112652
+    assert utils.count_lines(peak_file) == 138827

workflow/tests/test_diff_peaks.py

@@ -33,7 +33,7 @@ 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(os.path.join(test_output_path, 'ENCSR757EMK_vs_ENCSR729LGA_diffbind.bed'))
+    diffbind_file = test_output_path + 'ENCSR757EMK_vs_ENCSR729LGA_diffbind.csv'
     assert os.path.exists(diffbind_file)
-    assert utils.count_lines(diffbind_file) == 112652
+    assert utils.count_lines(diffbind_file) == 66201