Hi,
I'm trying to reproduce some Firecloud best practice workflows locally. However, some files used in the workflows could not be downloaded. For example, /usr/local/bin/hellbender-all-1.0.jar was used in Mutect best practice workflow. As the file does not appear in the list of downloadable Input files and the path of this file is not /cromwell_root/firecloud-tcga-open-access based (so could not get gs:// style address for gsutil), I couldn't find a way to download it yet. As the workflow could access this file, I think there might be some way to download it as well.
Also, "hellbender" is the code name of GATK 4. This file looks like a certain version of GATK 4. However, all versions of publicly available GATK 4 do not have the command "CreateEvenIntervals", which is used in the Mutect workflow. A command looking close to "CreateEvenIntervals" is "SplitIntervals". However, "SplitIntervals" seems only work for BAM/SAM/CRAM files, while "CreateEvenIntervals" works for interval files.
Any feedback are highly appreciated. Thank you.