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Double-pro. Running wireguard on docker assures that a native wireguard install won't conflict with docker. Keep those iptables in the same place.
I thought I would be the only one to try this. Would you share more details on your setup? I am interested because to me Wireguard is in the kernel so how could it be in a container.
Oh yeah. https://hub.docker.com/r/linuxserver/wireguard
Basically, docker can and does create network devices. It's as easy for it to create wg0's as it is to create networks for your other docker containers. If you're going to run wireguard and docker, you're better off to let docker handle the network routing and just run one of the various containers out there to stop them from fighting. That particular container is more general. You can run it client or server. Wg-easy, I believe is server-only, or even hide it inside other containers like docker-qbittorrent-wireguard, where it just hangs out and connects to whatever .conf you give it.
I did the whole thing in my early days selfhosting where I installed wireguard, docker, some apps, rebooted, everything breaks.
Install a wireguard container, configure it as you would, your apps, reboot... it still works, because docker isn't conflicting with native wg-quick. It's either this, or untangle and make an iptables setup permanent so when you reboot, it doesn't break again.