Expose XIMMER_REF in config.groovy rather than a env variable for docker run

[sclan]

This is a suggestion.

We have a docker platform that users can use the following input to run tools via docker image: input data files: (e.g,: *.bam, ref.fa, taget_region.bed) cmd: (e.g. ximmer -c config.groovy -o ./out -v) image: (e.g. ssadedin/ximmer)

Then the platform will run the following command: docker run -w /tmp -v ~/./out:/tmp ssadedin/ximmer ximmer -c config.groovy -o -v

The "docker run -w /tmp -v ~/./out:/tmp" is hard coded on our platform (and any output will be copied from /tmp to the final storage that users can access by the platform's post-processing mechanism). The rest of the command is provided by the user and the input data are copied to the home directory on the execution server.

Would be nice to allow users to specify the reference fasta file via the config file instead of passing it into the docker environment via "-e".