diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 0929f06a768306511f4b968fad2629c99933d24a..c81247ab8c0e40c75d4c3df9c36b8a6dd043e368 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -18,9 +18,9 @@ single_end_mouse:
   script:
   - nextflow run workflow/main.nf
   - pytest -m integration
-  - pytest --cov=./workflow/scripts 
+  - pytest --cov=./workflow/scripts
 
 paired_end_human:
   stage: integration
   script:
-  - nextflow run workflow/main.nf --designFile "$baseDir/../test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'
+  - nextflow run workflow/main.nf --designFile "$CI_PROJECT_DIR/test_data/design_ENCSR729LGA_PE.txt" --genome 'GRCh38'