Fix publishing in process_samples and process_batches

[DriesSchaumont]

Changelog

Fix publishing in process_samples and process_batches

Issue ticket number and link

~Closes #xxxx (Replace xxxx with the GitHub issue number)~

Checklist before requesting a review

• [x] I have performed a self-review of my code

• [x] Conforms to the Contributor's guide

• Check the correct box. Does this PR contain:

  • [ ] Breaking changes
  • [ ] New functionality
  • [ ] Major changes
  • [ ] Minor changes
  • [ ] Documentation
  • [x] Bug fixes

• [x] Proposed changes are described in the CHANGELOG.md

• [x] CI tests succeed!