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openpipelines-bio / openpipeline

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Capitalized modality names are not processed by full pipeline workflow #626

Open KaiWaldrant opened 5 months ago

KaiWaldrant commented 5 months ago

I had a Mudata where the modality name was capitalized "RNA" and the full pipeline workflow did not process the data and it was not clear as to why this happened. It only performed the process of split_mod, concat and merge.

https://production.nftower.jnj.com/orgs/JnJ-Core/workspaces/CS000253-Lysosomal-Storage-Biology/watch/53pbZSbGsmsPnr

DriesSchaumont commented 5 months ago

@KaiWaldrant Your modality should be lowercase: rna. Because it is uppercase , it is the modality is not recognized as being supported. The data is still goes through the dataflow, but no processing is being done.

KaiWaldrant commented 5 months ago

@DriesSchaumont I know, that is the issue for me. I had to troubleshoot why this was not anlyizing my data. It was not clear that the modality should be lower case. Some kind of message should be thrown if nothing is analyzed and/or the conversion tool should be altered to not allow uppercase because I added the modality in the conversion pipeline.

and another question should it be case dependent ?

DriesSchaumont commented 5 months ago

Thats another discussion. For the naming of the modalities, we follow the convention proposed by the single cell best practices. However, we could implement some functionality to customize this behavor. This needs to be discussed :)