common-workflow-language / common-workflow-language/user_guide

advanced lesson: inplace editing of existing files

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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#"
```

Contributor guide

Open the contributing guide

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