diff --git a/.github/workflows/add_iss2project.yml b/.github/workflows/add_iss2project.yml
index 30d57fc0..32c3d18e 100644
--- a/.github/workflows/add_iss2project.yml
+++ b/.github/workflows/add_iss2project.yml
@@ -10,7 +10,14 @@ jobs:
     name: Add issue to project
     runs-on: ubuntu-latest
     steps:
+      - name: Generate a token
+        id: generate-token
+        uses: actions/create-github-app-token@v1
+        with:
+          app-id: ${{ vars.NB_BOT_ID }}
+          private-key: ${{ secrets.NB_BOT_KEY }}
+
       - uses: actions/add-to-project@main
         with:
           project-url: https://github.com/orgs/neurobagel/projects/1
-          github-token: ${{ secrets.NB_PROJECT_PAT }}
+          github-token: ${{ steps.generate-token.outputs.token }}
diff --git a/.github/workflows/build_docker_nightly.yml b/.github/workflows/build_docker_nightly.yml
index f47c26fc..44fb74d2 100644
--- a/.github/workflows/build_docker_nightly.yml
+++ b/.github/workflows/build_docker_nightly.yml
@@ -12,6 +12,9 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v4
+        # Some repos have submodules that need to be part of the Docker image
+        with:
+          submodules: recursive
 
       - name: Login to Docker Hub
         uses: docker/login-action@v3
diff --git a/.github/workflows/build_docker_on_release.yml b/.github/workflows/build_docker_on_release.yml
index 7e3a1cc9..f229bcdc 100644
--- a/.github/workflows/build_docker_on_release.yml
+++ b/.github/workflows/build_docker_on_release.yml
@@ -11,6 +11,9 @@ jobs:
       -
         name: Checkout
         uses: actions/checkout@v4
+        # Some repos have submodules that need to be part of the Docker image
+        with:
+          submodules: recursive
       - 
         # The release event is a superset of the push tag event, 
         # so we expect two tags to be generated by docker/metadata-action