Make manta region bed index required

[VJalili]

The manta workflow fails if the index file does not exist; hence, following the discussion in #578, we are making this input required. Specifically:

The workflow fails to evaluate vm_disk_size and results in EXECUTOR_ERROR on CoA, which, since it occurs at the TES level, is a more challenging error to debug than task-level errors.

The alternative approach to the changes implemented in this PR is to adjust the vm_disk_size calculation to exclude the index file size from the calculation (which would not impact much since the file is small). The main drawback of this approach is that the /usr/local/bin/manta/bin/configManta.py script may fail if the optional file does not exist. Hence, making the file required seems a better option.

[mwalker174]

This looks good - the coding was a unnecessarily awkward. Do you want to do the same thing for the reference_index input also?

[VJalili]

Thank you, @mwalker174, for the prompt review!!

Do you want to do the same thing for the reference_index input also?

Yes, I will update that next.