diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c5a0ec4293a731f76b0f06c34a5e8bb8b965cc6c..99cab4a66e7220fb88fe21e0db9d7521b92254fa 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -56,8 +56,6 @@ single_end_single_control:
 single_end_diff:
   stage: multiple
   only:
-    - branches
-  except:
     - master
   script:
   - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_diff_SE.txt" --genome 'GRCm38' --astrocyte false
@@ -66,6 +64,8 @@ single_end_diff:
 
 paired_end_diff:
   only:
+    - branches
+  except:
     - master
   stage: multiple
   script:
diff --git a/workflow/tests/test_diff_peaks.py b/workflow/tests/test_diff_peaks.py
index 47940c0b2c103fda1445043915a70b3c4e1464d0..9e35c32c74010edfba2aa7e88f87fee63546354c 100644
--- a/workflow/tests/test_diff_peaks.py
+++ b/workflow/tests/test_diff_peaks.py
@@ -71,4 +71,4 @@ def test_diffbind_pairedend_single_rep():
         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) >= 65182
+    assert utils.count_lines(diffbind_file) >= 65124