amazon-genomics-cli icon indicating copy to clipboard operation
amazon-genomics-cli copied to clipboard

optionFileURL vs optionsFileURL in CromwellWESAdapter

Open mlin opened this issue 2 years ago • 3 comments

The docs and most examples use optionFileURL (singular) in the manifest. But CromwellWESAdapter looks for optionsFileURL (plural). Also, if we search this repo for optionsFileURL (plural), there are a few other examples.

I hit this trying to use optionFileURL to set default_runtime_attributes for a workflow whose tasks didn't specify cpu/memory requirements, and it didn't seem to be effective.

mlin avatar Jun 01 '22 08:06 mlin

@markjschreiber @wleepang ping

mlin avatar Jun 08 '22 23:06 mlin

What is the preference here?

  1. optionFile*
  2. optionsFile*

I think I prefer the plural since there are multiple options to set. We can then go through and normalize all uses, e.g. MAINFEST files and command line args.

wleepang avatar Jun 09 '22 01:06 wleepang

No strong preference from me, just the feature should work as documented =) (with tests?)

A meta-suggestion might be for AGC to show some warning if the MANIFEST.json has apparently extraneous keys.

mlin avatar Jun 09 '22 03:06 mlin