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Also, using nginx as a reverse proxy + letsencrypt is totally valid. I moved towards Traefik (https://github.com/traefik/traefik) which neatly integrates with containers and does all letsencrypt management for you (no need to maintain a separate letsencrypt service).
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This seems to definitely be the consensus! Someone on twitter linked me to a tool called Composerize which seems to be able to generate docker-compose configs directly from a docker run command which is exactly what I need.