diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7542f3cd4a72c01ad8ebc04a6fa74983f772c858..68bfb14153a9e42c3d0987bc70dbd1b29f5a04ca 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,3 +18,8 @@ single_end_mouse:
   script:
   - nextflow run workflow/main.nf
   - pytest -m integration
+
+paired_end_human:
+  stage: integration
+  script:
+  - nextflow run workflow/main.nf --designFile "test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'