Use subcommands for command line interface

[inodb]

It would be nice if we could use a more subcommand style interface as done here: https://github.com/genome-nexus/genome-nexus-cli

So e.g. to convert:

genome-nexus-annotation-pipeline convert variants.vcf > variants.maf

merge multiple MAFs:

genome-nexus-annotation-pipeline merge folder_with_mafs > output.maf

annotate a MAF:

genome-nexus-annotation-pipeline annotate maf test/data/minimal_example.in.txt [...more arguments] > test/data/minimal_example.out.txt

annotate a variant:

genome-nexus-annotation-pipeline annotate variant 17:g.41242962_41242963insGA > variant.json

show full help of all commands:

$ genome-nexus-annotation-pipeline --help
    convert
    merge
    annotate

The current pipeline arguments are idiosyncratic to our internal annotation processes and not super user friendly for external users