common-workflow-language / common-workflow-language/user_guide
advanced lesson: inplace editing of existing files
- Langage dominant
- Common Workflow Language
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Description
This lesson needs to make very clear that only some CWL engines support this extension, but that it is planned for CWL v1.1
Known implementors:
- cwlref-runner
- arvados
Need to check
- [ ] toil-cwl-runner
- [ ] rabix executor
Use case: "ms" measurement sets from radio astronomy (essentially they are very large (terabyte) databases spread across many files in a directory)
If you need to manipulate a dataset but don't care if it is copied use:
``` cwl
requirements:
InitialWorkDirRequirement:
listing:
- entry: $(inputs.dataset)
writable: true
inputs:
dataset: Directory
```
If you do care about not copying (manipulate in place):
``` cwl
requirements:
InitialWorkDirRequirement:
listing:
- entry: $(inputs.dataset)
writable: true
cwltool:InplaceUpdateRequirement:
inplaceUpdate: true
inputs:
dataset: Directory
$namespaces:
cwltool: "http://commonwl.org/cwltool#"
```
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