Small fixes in autoclean_sftp and bioinfo-doc. Reverted excel_generator.py

[Shettland]

PR checklist

• I included small fixes in autoclean_sftp and bioinfo-doc modules that appeared with the new release 2.0.0. Also included a new user in sftp_user.json and reverted excel_generator.py to its previous state with an argument to indicate when to merge lineage tables, as the latest changes were not flexible for those situations where there is no reason to merge them.
• Make sure your code lints (black and flake8).
• If a new tamplate was added make sure:
  • Template's schema is added in templates/services.json.
  • Template's pipeline's documentation in assets/reports/md/template.md is added.
  • Results Documentation in assets/reports/results/template.md is updated.
• CHANGELOG.md is updated.
• README.md is updated (including new tool citations and authors/contributors).
• If you know a new user was added to the SFTP, make sure you added it to templates/sftp_user.json