angelolab / toffy

Scripts for interacting with and generating data from the commercial MIBIScope
MIT License
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Add fallback protection to Rosetta pipeline #375

Open alex-l-kong opened 1 year ago

alex-l-kong commented 1 year ago

Is your feature request related to a problem? Please describe.

If the Rosetta pipeline crashes in the middle of a process, there isn't a recovery scheme in place to prevent needing to re-run it in its entirety. The functions where this has been problematic:

Even over Ethernet connection to the NAS, certain processes can still take several hours.

Describe the solution you'd like

These functions, and the notebook itself, need to bypass files and directories that have already been created. This involves adding additional checks similar to what we do in the Pixie pipeline.

ngreenwald commented 1 year ago

I think #403 should help to speed up the testing workflow. This would still be worth doing for the actual compensation step though, since is run across the entire cohort.