Try <<-EOF with tabs

.gitlab-ci.yml

@@ -57,11 +57,12 @@ deploy:
   stage: deploy
   script:
     - rsync -r --delete-after --quiet ./ $SSH_USER@$DEPLOY_HOST::apilab/
-    - ssh $SSH_USER@$DEPLOY_HOST <<EOF
-      . ~/.bashrc
-      . ~/.nvm/nvm.sh
-      nvm use stable
-      pm2 restart apilab
+    # The EOF heredoc needs to use tabs if we want to indent things
+    - ssh $SSH_USER@$DEPLOY_HOST <<-EOF
+      	. ~/.bashrc
+      	. ~/.nvm/nvm.sh
+      	nvm use stable
+      	pm2 restart apilab
       EOF
   environment:
     name: production