Pointing Cromwell to local EBS mounted storage on AWS Batch
Somebody helped me with this one through other channels, but I wanted to make it publicly available:
Make a tarball of the STAR index. The option --strip-components=1 strips the first level of the path from the untarred items; thus, the expected tarball was made with something like
tar -cvf ${star_index} the_star_index_directory/

Then point Cromwell/WDL to the tarball, e.g. on S3. The GTEx container will unwrap the tarball on the fly during execution.