git clone https://github.com/letsencrypt/letsencrypt cd letsencrypt/ ./letsencrypt-auto (ignore the 'error'. It's because you don't run apache)

/root/.local/share/letsencrypt/bin/letsencrypt certonly --webroot -w /var/www/example.com/public -d www.example.com -d example.com (uses the public directory for ownership check, and creates a cert for www.example.com + example.com)

Then in your /etc/nginx/sites-enabled/example.com:

/etc/letsencrypt/live/www.example.com/fullchain.pem; /etc/letsencrypt/live/www.example.com/privkey.pem;

Sorry.. you're asking for automation