diff --git a/.github/workflows/create-lint-wf.yml b/.github/workflows/create-lint-wf.yml
index 30920e7431..95c92f5fe2 100644
--- a/.github/workflows/create-lint-wf.yml
+++ b/.github/workflows/create-lint-wf.yml
@@ -80,8 +80,12 @@ jobs:
       # - name: nf-core licences
       #   run: nf-core --log-file log.txt licences nf-core-testpipeline
 
+      # Remove any unstaged changes from update etc and try to sync pipeline
       - name: nf-core sync
-        run: nf-core --log-file log.txt sync --dir nf-core-testpipeline/
+        run: |
+          rm -r modules
+          git checkout .
+          nf-core --log-file log.txt sync --dir nf-core-testpipeline/
 
       - name: nf-core schema
         run: nf-core --log-file log.txt schema build --dir nf-core-testpipeline/ --no-prompts