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getwilds / rcromwell

R client for interacting with Cromwell with WDL workflows
http://getwilds.org/rcromwell/
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Batch file - to - json conversion #1

Open vortexing opened 4 years ago

vortexing commented 4 years ago

Should add a function to convert a data frame full of manifest/batch information into a single, well formatted json for a workflow, so that it'd be easier for users to use a structured list of inputs to a workflow but then also make the workflow truly reproducible from a Cromwell perspective. It currently will not re-load a batch file if it has the same name as the one before unless you turn off call caching. Perhaps there's a way to turn off call caching for one task but until then, adjust.

sckott commented 5 months ago

@vortexing still think we should address this or no?

vortexing commented 5 months ago

I think this is a future feature or new tool - a tool that folks can use to take their excel spreadsheet in the lab or an R data frame and convert it into a custom Array[struct] and export a validate-able json.

sckott commented 5 months ago

okay, sounds good. and makes sense to leave here until figuring out whether and where to do this