lynis VS Cryptomator

Linux has (free) tools to improve security and detect/remove malware: Lynis,Chkrootkit,Rkhunter,ClamAV,Vuls,LMD,radare2,Yara,ntopng,maltrail,Snort,Suricata...

What I would do in your place is run this https://github.com/CISOfy/lynis and follow some of the instructions.

https://github.com/CISOfy/Lynis (Linux hardening)

Linux security audit scanner

the best way to do this is with https://cryptomator.org

Before putting anything on a cloud service I would recommend 3rd party tools, like Cryptomator, to encrypt folders and such, then upload to a cloud service.

I use Cryptomator - https://cryptomator.org

I've used countless encryption "schemes" over the years, from True/Vera-Crypt to encrypted sparse bundles/images, and none have ever really felt right.

These days i tend to use Cryptomator[0] instead. It accomplishes what none of the others could do, which is transparent encryption across devices.

With Cryptomator, i simply create a vault somewhere in the cloud, stuff data in it, and i can access it from my laptop, phone or tablet, and not think much about it. It integrates into the normal file browsing APIs, and doesn't get in the way.

Because it does "per file" encryption, it also doesn't need to download a 20-100MB chunk from the cloud before decrypting, so it's rather fast (depending on file size of course).

[0]: https://cryptomator.org/

Cryptomator's arguably the most popular encryption software for cloud storage (you can give yourself zero-knowledge encryption by using them) - it's actually what they specialize & focus on (cloud encryption). It's 100% open source and Free to use on computers. On phones I believe it's just a 1-time fee of a few bucks ($13-14, then you have it forever) - note: their iOS offering is still new, so may be a bit unpolished at the moment.

This is the solution: https://cryptomator.org/

Cryptomator. It is made for uploading files securely to cloud storage, but works locally, is easy to use, and completely free for your use case.