Enabling HTTPS after using the install script

Nextcloud version (eg, 20.0.5): 21.0.1
Operating system and version (eg, Ubuntu 20.04): Ubuntu 20.043
Apache or nginx version (eg, Apache 2.4.25): 2.4.41

The issue you are facing: I installed Nextcloud using the install script, and I’m trying to enable HTTPS using Letsencrypt. I ran the certbot wizard for apache, and it’s saying the error below

No vhost exists with servername or alias of sub.domain.com. No vhost was selected. Please specify ServerName or ServerAlias in the Apache config.
No vhost selected

What .conf file am I supposed to edit in /etc/apache2? Looking at the documents, it doesn’t say what file to change

Edit: I managed to get LE installed by creating a sub.domain.com.conf file in sites-available and enabling it, but Nextcloud is still using the self signed cert and not the new one from LE. How can I change that?

Edit2: Managed to fix it by editing the cert paths to the LE certs in the -tls- conf file the install script makes. For whatever reason, apache is only using that single conf file, the ones LE makes and the one I manually made were ignored.