Create your config.yml and download directory in a local folder in your computer and attach this as a volume to the container.
docker build -t flexget .
mkdir -p ~/flexget/
docker run -it --rm --name=flexget -v ~/flexget/:/root/.flexget/ flexget"
docker run -it --rm --name=flexget -v ~/flexget:/root/.flexget/ mjimeneznet/docker-flexget:latest"