diff --git a/.github/workflows/gh-pages.yml b/.github/workflows/gh-pages.yml
index a8f7559..ca84e9b 100644
--- a/.github/workflows/gh-pages.yml
+++ b/.github/workflows/gh-pages.yml
@@ -27,8 +27,8 @@ jobs:
 
       - name: Build the documentation
         run: |
-          sphinx-apidoc -o docs/source/ protac_degradation_predictor
-          sphinx-build docs docs/_build/html
+          sphinx-apidoc -o ./docs/source/ protac_degradation_predictor --separate
+          sphinx-build ./docs ./docs/_build/html
 
       - name: Deploy to GitHub Pages
         uses: peaceiris/actions-gh-pages@v3