diff --git a/.github/workflows/tcoffee.yml b/.github/workflows/tcoffee.yml
index 59b7b04e..fedb6790 100644
--- a/.github/workflows/tcoffee.yml
+++ b/.github/workflows/tcoffee.yml
@@ -11,8 +11,13 @@ jobs:
     steps:
 
     # Check out the repository
-    - uses: actions/checkout@v1
-      submodules: true
+    - uses: actions/checkout@v2
+    - name: Checkout submodules
+      shell: bash
+      run: |
+          auth_header="$(git config --local --get http.https://github.com/.extraheader)"
+          git submodule sync --recursive
+          git -c "http.extraheader=$auth_header" -c protocol.version=2 submodule update --init --force --recursive --depth=1
 
     - name: Install Nextflow
       run: |