CombineGVCFs won't work due to lack of vcf index inputs

[rickymagner]

I tried using the CombineGVCFs auto-generated wdl but ran into issues with localizing the index files for the input vcfs. Here is the error:

A USER ERROR has occurred: An index is required but was not found for file /cromwell_root/broad-gotc-test-storage/germline_single_sample/wgs/load/truth/develop/NA12878/NA12878.g.vcf.gz. 
Support for unindexed block-compressed files has been temporarily disabled. Try running IndexFeatureFile on the input.

This always happens when one forgets to include the vcf indices as inputs into the wdl since they need to be localized along with the actual vcfs. However, this wdl doesn't have the option to pass them in, making it essentially impossible to use right out of the box. The simple fix is to just put index inputs into the task, but maybe it's worth doing at the level of the auto-generating code to ensure other similar tasks are able to run without the user needing to manually override them.

[rickymagner]

Closing this issue because it has been remigrated as appropriate to here.