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tests: expand excerpts into full files & misc cleanups #172

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Feb 12, 2022
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tests: expand excerpts into full files & misc cleanups #172

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f4f9ca9
tests: expand excerpts into full files
mr-c Feb 11, 2022
b71850d
parse out doc string from {,parameter_}meta
mr-c Feb 12, 2022
b6e66a3
sort generated CWL more sensibly
mr-c Feb 12, 2022
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18 changes: 17 additions & 1 deletion README.md
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Expand Up @@ -66,13 +66,29 @@ To output the CWL version to your terminal/stdout.
wdl2cwl path_to_workflow.wdl --output path_to_new_workflow.cwl
```

## Limitations
## Temporary Limitations

WDL features not yet supported
- [Scatter](https://github.com/common-workflow-lab/wdl-cwl-translator/issues/146)
- [Map](https://github.com/common-workflow-lab/wdl-cwl-translator/issues/77) types
- [Nested structs](https://github.com/common-workflow-lab/wdl-cwl-translator/issues/158)

## Incompatibilities possibly requiring manual intervention

1. Dynamic specification of Docker containers. As of CWL v1.2, CWL's DockerRequirement
has no support for dynamic specifications, only fixed values. If a WDL task has a
`runtime.docker` that references an input with a default value, then `wdl2cwl` does
try to copy that to the CWL `DockerRequirement.dockerPull`.

If changing the software container is needed, there are several workarounds:
1. Use workflow runner/engine provided overrides: many CWL runners
(including those based upon the CWL reference runner, `cwltool`) support overriding
requirements at any level at run time. See
https://github.com/common-workflow-language/cwltool#overriding-workflow-requirements-at-load-time
2. Manually override the `DockerRequirement` in `hints` by specifying your own container
at the CWL workflow step level under `requirements`
3. Manually editing the CommandLineTool definition yourself.

### File Localization

(Open)WDL assumes that users will configure localization by placing
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