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mpc-bioinformatics / McQuaC

Transform the Quality Control workflow from Knime into a workflow in Nextflow
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Spikein protein columns in quality-control.csv #50

Closed di-hardt closed 4 months ago

di-hardt commented 6 months ago

It is not ideal to put each spikein protein into a separate column of the quality-control.csv. That would mean the database table needs to be customized depending on your list of spikeins or the database importer needs to take care of it.

I would suggest to use only one column spikeins containting a Dictionary in JSON-format, where each key is a spikein while the value is the former cell value, e.g.

... spikeins ...
... {"FIXED_MPCSPIKE1_PEP_old-isa01_MZ_457.2834_RT_2439": <VALUE>, "FIXED_MPCSPIKE2_PEP_old-isa02_MZ_895.9493_RT_4212": <VALUE>, ...} ...

This makes it much more generic and database friendly.

KarinSchork commented 6 months ago

Maybe we could export (maybe in the visualization script?) then a more human-readable form of the spike-ins for the TAs?

KarinSchork commented 4 months ago

It is know solved by creating a pickle out of the spike-in csv.