Allow dependencies file without an options.json

[lbergelson]

Currently you can't submit a job that has a dependencies.zip without also including an options.json.

Currently you can work around this issue by submitting an options.json with no keys.

options.json

{}

It would be good if you could skip the options.json when you don't need it.

[jonn-smith]

Without making assumptions about filenames, we can use file to query the file arguments and get their types:

file compareHaplotypeCallerRuns_Subworkflows.zip
/compareHaplotypeCallerRuns_Subworkflows.zip: Zip archive data, at least v2.0 to extract

We can grep for Zip archive data in the output and handle the positional args accordingly.