common-workflow-language / common-workflow-language/cwltool
Do not copy in-place updated files to output directory
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- Dominant language
- Python
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- 376
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- Avg merge
- 2d 7h
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- 12
Description
## Expected Behavior
CWLTool should create symbolic links in the output directory to files/directories that are updated in-place.
## Actual Behavior
CWLTool copies files/directories that are updated in-place to the output directory.
This is an optimisation and not really a bug. See https://gitter.im/bd2k-genomics-toil/Lobby?at=63d25acd7740c84e493311f4
## Your Environment
* cwltool version: 3.1.20221008225030
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