CombineGVCFs auto-generated workflow is missing vcf indices as inputs

[rickymagner]

Bug Report

Affected tool(s) or class(es)

CombineGVCFs

Affected version(s)

• Latest public release version [4.2.5.0]
• Latest master branch as of [date of test?]

Description

The auto-generated wdl for CombineGVCFs on dockstore won't work because it doesn't have any inputs for the indices of the input vcfs. This means GATK cannot access the vcf indices because they never get localized, so the workflow fails.

Steps to reproduce

Take any vcfs and run them through the workflow to get an error about missing indices.

Expected behavior

Including the indices in the task inputs will allow them to get localized along with the vcfs so GATK can operate normally.

Actual behavior

You get an error saying it requires index files to proceed.

[cmnbroad]

For variant inputs, there is no explicit arg for the index inputs (like there is for read inputs), so for variants the index needs to be added to the input annotation as a companion file.