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

Directly wrapping Python/Ruby/Perl functions in CWL

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#844 3 comments 0 reactions 0 assignees View on GitHub
make running scripts easier
Dominant language
Common Workflow Language
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Description

Apologies if this point is addressed elsewhere and I've missed a previous issue / listserv post. If there's a past discussion of this somewhere that addresses this, feel free to point me to where it has occurred.

In [DigDag](https://www.digdag.io/), it appears that you can directly use individual Python/Ruby functions as nodes in a workflow (see [here](http://docs.digdag.io/operators/scripting.html)). While this is currently possible in CWL by combining a Command Line Tool with a wrapper script using Python's argparse, it is a bit unwieldy / not as seamless as being able to directly specify in the workflow that you want to invoke a specific Python function. Are there any plans in the works to create a "Python Tool" or "Ruby Tool" specification for CWL so that end-users of CWL-based tools wouldn't need to go through the extra step of wrapping Python/Ruby functions with argparse?

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