assemble_refbased: indelrealigner fails on zero reads

[dpark01]

In the case that no reads align, our code correctly deals with producing empty bams from minimap2 and picard markduplicates, but is failing on gatk indelrealigner. We would likely need to add a defensive wrapper around the indelrealigner call to handle the zero reads aligned case.

Example failure:
https://job-manager.dsde-prod.broadinstitute.org/jobs/8a8e4123-049c-4f5d-bc95-cb2b936778c2