Running a command in a container and copying resultying files to host in one docker call

Question

I'm trying to use docker to run a PLINK command. PLINK uses intermediate files to store information required for subsequent commands. For what I am trying to do, I can't run all the PLINK commands in a single docker call so the only workaround I thought of is to copy the intermediate files from the running docker container into a host directory and the mount that directory in subsequent calls. Has anyone tried to do this before? How should I go about running the command in the container AND copying the contents of the working directory in the container to the host directory all in one line?