Template issues

[saramonzon]

• Closes Update SFTP copy files #235
• Closes Remove ad-hoc node in exometrio 03-annotation lablog #228
• Closes Remove --save_align_intermeds from rna-seq template #196

PR checklist

• This comment contains a description of changes (with reason).
• 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