We were caching already devirtualized files in the virtualized-to-devirtualized cache, which caused conflicts when the task/job cleaned up its files but the workflow attempts to access it again from the "virtualized" url.
This separates the caching a bit so it only adds it to the cache when we actually have a virtualized file to devirtualize.
This also lets the devirtualization step start using the cache, which it wasn't doing before.
[ ] New functions or classes without informative docstrings.
[ ] Changes to semantics not reflected in the relevant docstrings.
[ ] New or changed command line options for Toil workflows that are not reflected in docs/running/{cliOptions,cwl,wdl}.rst
[ ] New features without tests.
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Closes #4959
We were caching already devirtualized files in the virtualized-to-devirtualized cache, which caused conflicts when the task/job cleaned up its files but the workflow attempts to access it again from the "virtualized" url.
This separates the caching a bit so it only adds it to the cache when we actually have a virtualized file to devirtualize. This also lets the devirtualization step start using the cache, which it wasn't doing before.
Changelog Entry
To be copied to the draft changelog by merger:
Reviewer Checklist
issues/XXXX-fix-the-thing
in the Toil repo, or from an external repo.camelCase
that want to be insnake_case
.docs/running/{cliOptions,cwl,wdl}.rst
Merger Checklist