Please have a look at the certbot-dns-cloudflare documentation first.

Procedure :

• Edit domains in the compose file
• Edit CloudFlare credentials in cloudflare.ini file (generate using https://dash.cloudflare.com/?to=/:account/profile/api-tokens)
• Run certbot only and wait for certificates to be generated : docker-compose up -d mycertbot
• When certificates are generated, run your services : docker-compose up -d