diff --git a/.github/workflows/cutadapt.yml b/.github/workflows/cutadapt.yml
index 81c734ad..0aa773d8 100644
--- a/.github/workflows/cutadapt.yml
+++ b/.github/workflows/cutadapt.yml
@@ -10,8 +10,13 @@ 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: |