diff --git a/.github/workflows/compatibility-test copy.yaml b/.github/workflows/compatibility-test copy.yaml
deleted file mode 100644
index 1c7cff8..0000000
--- a/.github/workflows/compatibility-test copy.yaml	
+++ /dev/null
@@ -1,55 +0,0 @@
-name: Check compatibility of latest
-
-on:
-  schedule:
-    # * is a special character in YAML so you have to quote this string
-    - cron:  '31 5,17 * * *'
-  workflow_dispatch:
-
-jobs:
-  Neurobagel-latest:
-    runs-on: ubuntu-latest
-        
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Rename files
-        working-directory: .
-        run: |
-          cp template.env .env
-          cp local_nb_nodes.template.json local_nb_nodes.json
-      
-      - name: Run docker compose
-        working-directory: .
-        run: |
-          docker compose --profile full_stack up -d
-
-      - name: Set up node env
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-      
-      - name: Install cypress
-        run: npm install
-
-      - name: wait for graph set up
-        working-directory: ./scripts
-        run: |
-          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
-            :
-          done
-          echo "Finished setting up the Neurobagel graph backend."
-
-      - name: Run end to end tests
-        uses: cypress-io/github-action@v6
-        with:
-          wait-on: http://localhost:3000
-          component: false
-
-      - name: Latest broke, tell someone
-        if: ${{ failure() }}
-        run: |
-          curl -X POST -H 'Content-type: application/json' --data '{"text":"Neurobagel latest broke! Please check https://github.com/neurobagel/recipes/actions and resolve the incompatible versions!"}' ${{ secrets.NB_SLACK_WEBHOOK }}
-
-
diff --git a/.github/workflows/compatibility-test.yaml b/.github/workflows/compatibility-test.yaml
deleted file mode 100644
index e7c6acc..0000000
--- a/.github/workflows/compatibility-test.yaml
+++ /dev/null
@@ -1,48 +0,0 @@
-name: compatibility tests
-
-on:
-  workflow_dispatch:
-
-jobs:
-  Compatibility-test:
-    runs-on: ubuntu-latest
-        
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-
-      - name: Rename files
-        working-directory: .
-        run: |
-          cp template.env .env
-          cp local_nb_nodes.template.json local_nb_nodes.json
-          sed -i 's/latest/nightly/g' .env
-      
-      - name: Run docker compose
-        working-directory: .
-        run: |
-          docker compose --profile full_stack up -d
-
-      - name: Set up node env
-        uses: actions/setup-node@v4
-        with:
-          node-version: 20
-      
-      - name: Install cypress
-        run: npm install
-
-      - name: wait for graph set up
-        working-directory: ./scripts
-        run: |
-          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
-            :
-          done
-          echo "Finished setting up the Neurobagel graph backend."
-
-      - name: Run end to end tests
-        uses: cypress-io/github-action@v6
-        with:
-          wait-on: http://localhost:3000
-          component: false
-
-
diff --git a/.github/workflows/compatibility.yaml b/.github/workflows/compatibility.yaml
new file mode 100644
index 0000000..68a5c34
--- /dev/null
+++ b/.github/workflows/compatibility.yaml
@@ -0,0 +1,120 @@
+name: Compatibility of
+
+on:
+  workflow_dispatch:
+  schedule:
+    - cron: '21 5,17 * * *'
+
+jobs:
+  latest:
+    runs-on: ubuntu-latest
+        
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Rename files
+        working-directory: .
+        run: |
+          cp template.env .env
+          cp local_nb_nodes.template.json local_nb_nodes.json
+      
+      - name: Run docker compose
+        working-directory: .
+        run: |
+          docker compose --profile full_stack up -d
+
+      - name: Set up node env
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      
+      - name: Install cypress
+        run: npm install
+
+      - name: wait for graph set up
+        working-directory: ./scripts
+        run: |
+          # The logs are written at the end of the setup at the moment, so we have to wait for the file to exist
+          while [ ! -f ./logs/DEPLOY.log ]; do
+            :
+          done
+          # Once the file is there, we want to wait for the message that the setup is done
+          echo "We think the file exists now!"
+          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
+            :
+          done
+          echo "Finished setting up the Neurobagel graph backend."
+
+      - name: Run end to end tests
+        uses: cypress-io/github-action@v6
+        with:
+          wait-on: http://localhost:3000
+          component: false
+
+      - name: Latest failed, tell someone
+        if: ${{ failure() }}
+        run: |
+          curl -X POST -H 'Content-type: application/json' --data '{"text":"Neurobagel latest version compatibility test failed! Please check https://github.com/neurobagel/recipes/actions and resolve the incompatible versions!"}' ${{ secrets.NB_SLACK_WEBHOOK }}
+
+      - name: Clean up again
+        working-directory: .
+        run: |
+          docker compose --profile full_stack down
+
+  nightly:
+    runs-on: ubuntu-latest
+        
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Rename files
+        working-directory: .
+        run: |
+          cp template.env .env
+          cp local_nb_nodes.template.json local_nb_nodes.json
+          sed -i 's/latest/nightly/g' .env
+      
+      - name: Run docker compose
+        working-directory: .
+        run: |
+          docker compose --profile full_stack up -d
+
+      - name: Set up node env
+        uses: actions/setup-node@v4
+        with:
+          node-version: 20
+      
+      - name: Install cypress
+        run: npm install
+
+      - name: wait for graph set up
+        working-directory: ./scripts
+        run: |
+          # The logs are written at the end of the setup at the moment, so we have to wait for the file to exist
+          while [ ! -f ./logs/DEPLOY.log ]; do
+            :
+          done
+          # Once the file is there, we want to wait for the message that the setup is done
+          echo "We think the file exists now!"
+          while ! tail -n 0 -f ./logs/DEPLOY.log | grep -q "Finished setting up the Neurobagel graph backend."; do
+            :
+          done
+          echo "Finished setting up the Neurobagel graph backend."
+
+      - name: Run end to end tests
+        uses: cypress-io/github-action@v6
+        with:
+          wait-on: http://localhost:3000
+          component: false
+
+      - name: Nightly failed, tell someone
+        if: ${{ failure() }}
+        run: |
+          curl -X POST -H 'Content-type: application/json' --data '{"text":"Neurobagel nightly version compatibility test failed!"}' ${{ secrets.NB_SLACK_WEBHOOK }}
+
+      - name: Clean up
+        working-directory: .
+        run: |
+          docker compose --profile full_stack down
diff --git a/cypress/e2e/simple-test.js b/cypress/e2e/simple-test.cy.js
similarity index 91%
rename from cypress/e2e/simple-test.js
rename to cypress/e2e/simple-test.cy.js
index e7dab8e..8498cfb 100644
--- a/cypress/e2e/simple-test.js
+++ b/cypress/e2e/simple-test.cy.js
@@ -14,7 +14,7 @@ describe('Full stack e2e', () => {
     });
   });
   it("Federation API", () => {
-    cy.request("localhost:8000/query/?node=local graph 1").as("query");
+    cy.request("localhost:8080/query/?node=http://api:8000/").as("query");
     cy.get("@query").should((response) => {
       expect(response.status).to.eq(200);
     });