Updated pipelines paths where necessary

[victor5lm]

PR checklist

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

PR description

This PR updates all files that use the /pipelines/ folder, so that all paths are adapted to its new structure. Plus, plasmidID's lablog is updated.