Fixes in archive module and plasmidID docs

Formatted viralrecon markdown
Added plasmidID docs. Closes: https://github.com/BU-ISCIII/BU-ISCIII/issues/52 and related to https://github.com/BU-ISCIII/buisciii-tools/issues/4
Fixes in archive module for scout option

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:
- [x] Template's schema is added in templates/services.json.
- [x] Template's pipeline's documentation in assets/reports/md/template.md is added.
- [x] 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