diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 84f147bc84ed3423ab6947bf6065699f0966a874..cbf3cd81d79fb7f920e121e9f54d96cb6ca8cb12 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,6 +6,7 @@ variables:
 
 before_script:
   - module load nextflow/0.27.6
+  - git submodule update --init --recursive
   - git submodule sync --recursive
 
 stages: