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nadeemlab / SPT

Spatial profiling toolbox for spatial characterization of tumor immune microenvironment in multiplex images
https://oncopathtk.org
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Counts files to db migration #295

Closed wooferclaw closed 9 months ago

wooferclaw commented 9 months ago

not yet tested

jimmymathews commented 9 months ago

I have moved the lines, that actually invoke caching, to the end of the tabular import workflow (main.nf). Now the ondemand containers (start.py) should rarely have to actually do the caching on their own. They still check to see if the cache is present, and recreate it if not, but in normal circumstances this should happen before the service containers are created.

jimmymathews commented 9 months ago

All tests pass for me.

jimmymathews commented 9 months ago

After this is merged we will need to update spt-dashboard to stop using mounted volumes. We should also do a fresh dataset import using the new functionality.

jimmymathews commented 9 months ago

Addresses #221 .