Change the submodule strategy.

.gitlab-ci.yml

 # Gitlab CI Script for astrocyte/rnaseq
 # Brandi L. Cantarel - 2017
 
+variables:
+  GIT_SUBMODULE_STRATEGY: recursive
+
 before_script:
   - module load nextflow/20.01.0
   - module load singularity/3.0.2
-  - git submodule sync --recursive
-  - git submodule update --init --recursive
 
 stages:
   - integration