Which directory? frappe_docker directory, the repo that was cloned will not have any data.
docker data is in /var/lib/docker, that will have so that volumes including db volumes.
You can use restic which is part of image, How to backup with restic to S3 compatible storage
With restic you can use multiple backends to take and restore snapshots. You need to do is bench --site all backup and create restic snapshot of sites directory, that way you can take backup of updated files.
Example backup commands custom_containers/compose/erpnext-backup.yml at main · castlecraft/custom_containers · GitHub