certbot certonly --webroot --webroot-path="/home/domain/public_html/subdomain/public/"

Add the SSL Virtual Host to your conf.d virtual host file

<VirtualHost YOUR_IP:443>
ServerName YOUR_HOSTNAME:443

    DocumentRoot /home/domain/public_html/subdomain/public/

    <Directory /home/domain/public_html/subdomain/public>
        Options Indexes FollowSymLinks Includes
        Require all granted
        AllowOverride All
        Order allow,deny
        Allow from all
    </Directory>

  SSLEngine on
  SSLCertificateFile /etc/letsencrypt/live/domain/fullchain.pem
  SSLCertificateKeyFile /etc/letsencrypt/live/domain/privkey.pem

</VirtualHost>

To non-interactively renew *all* of your certificates, run
   "certbot renew"