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Define a strategy to run user-defined pipelines using WDL #1280

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ambrosejcarr opened this issue Apr 25, 2019 · 0 comments · Fixed by #1364
Closed

Define a strategy to run user-defined pipelines using WDL #1280

ambrosejcarr opened this issue Apr 25, 2019 · 0 comments · Fixed by #1364
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@ambrosejcarr @shanaxel42
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@ambrosejcarr
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Currently we have had some success by inlining python code, however it would be ideal to refine this to shunt more of the code into the repository.

See https://github.com/spacetx/starfish/tree/ajc-wdl-smfish for example workflows
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Creating a standard starfish.wdl that can be run with any recipe file spacetx/starfish
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@neuromusic @ambrosejcarr @shanaxel42