Fixed clean module - Githubissues

Fixed clean module:

Corrected purge_files function. Now it is able to properly find and remove the files set in services.json for every service.
Renaming stage moved from clean to rename_nocopy option in order to avoid non-renamed folders being copied from services_and_colaborations to sftp.
Updated services.json file with correct file paths and file names for some services.

Closes #199 Closes #221 Closes #233 Related #223

PR checklist

[x] 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.
[x] 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