diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml
index 62e4a82..aab4666 100644
--- a/.github/workflows/main.yml
+++ b/.github/workflows/main.yml
@@ -18,22 +18,13 @@ on:
   pull_request:
     branches:
       - main
-    paths-ignore: # ignore auto-generated files, only run when source files change
-      - docs/contrib.md
-      - docs/fluorescent_probes.md
-      - docs/index.md
-      - docs/protocols.md
-      - docs/publications.md
-      - docs/reagent_resources.md
-      - docs/the_who.md
-      - docs/videos.md
-      - docs/data_and_software.md
   # Enable manual running of workflow, so that if the validation or
   # markdown generation code changes we can force execution
   workflow_dispatch:
 
 jobs:
-  preliminary_test: # run all pre-commit tests (see .pre-commit-config.yaml)
+  preliminary_test:
+    # run all pre-commit tests (see .pre-commit-config.yaml)
     runs-on: macos-latest
     steps:
     - uses: actions/checkout@v4
@@ -43,10 +34,37 @@ jobs:
       uses: actions/setup-python@v5
       with:
         python-version: "3.10"
-    - name: Run pre-commit tests 
+    - name: Run pre-commit tests
       run: |
         pip install pre-commit
         pre-commit run --all-files
+  pr_preliminary_test:
+    # check that no auto-generated file was modified in a PR on main so just check we're dealing with a PR
+    # (workflow "on" event settings are all on main branch)
+    needs: preliminary_test
+    if: github.event_name == 'pull_request'
+    runs-on: macos-latest
+    steps:
+    - uses: actions/checkout@v4
+    - uses: dorny/paths-filter@v3
+      id: filter
+      with:
+        filters: |
+          autogenerated_docs:
+            - docs/contrib.md
+            - docs/fluorescent_probes.md
+            - docs/index.md
+            - docs/protocols.md
+            - docs/publications.md
+            - docs/reagent_resources.md
+            - docs/the_who.md
+            - docs/videos.md
+            - docs/data_and_software.md
+    - name: modified autogenerated docs # succeed if no auto-generated files modified, otherwise fail
+      if: steps.filter.outputs.autogenerated_docs != 'false'
+      run: |
+        echo "The pull request includes changes to auto-generated files, this is not allowed. Please modify the relevant files in the docs_in and data directories."
+        exit 1
   validate_data:
     needs: preliminary_test
     runs-on: macos-latest
@@ -70,7 +88,8 @@ jobs:
         validate_videos data/videos.csv .github/data_validation_configs/videos.json .zenodo.json
         validate_image_resources data/image_resources.csv .github/data_validation_configs/image_resources.json docs/supporting_material
         validate_reagent_resources data/reagent_resources.csv .github/data_validation_configs/reagent_resources.json .zenodo.json data/vendor_urls.csv docs/supporting_material
-  data_2_md: # run the data to markdown updates only when pushing to the main branch or forced execution via workflow_dispatch
+  data_2_md:
+    # run the data to markdown updates only when pushing to the main branch or forced execution via workflow_dispatch
     needs: validate_data
     if: ${{ github.event_name == 'push' && github.ref == 'refs/heads/main' || github.event_name == 'workflow_dispatch'}}
     runs-on: macos-latest