Currently it is possible with the docker-workflow-plugin to provide arguments to the docker run command. However these are inserted into the command line before the image name.
There does not appear to be any way to specify arguments to appear after the image name; so currently it does not appear to be possible to provide arguments to the container's entrypoint (without creating a custom Dockerfile with those commands built in).

e.g. the scenario I would like to achieve is the equivalent of this command line:

docker run --link=mysql-container:mysql --link=mongo-container:mongo maven:3.3.3-jdk-7 clean install

Currently I could run

docker.image('maven:3.3.3-jdk-7').run("--link=${mysql.id}:mysql --link=${mongo.id}:mongo");

which would take care of the arguments to docker, but would not pass 'clean install' arguments to the mvn command which is maven:3.3.3-jdk-7's entrypoint.

Currently the only way I see to do this is to use 'sh' to run the docker command line, and not use the docker-workflow-plugin for this container.