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maxplanck-ie / dissectBCL

demultiplexing pipeline
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email - parkour organism #205

Open WardDeb opened 2 weeks ago

WardDeb commented 2 weeks ago

Accommodate new parkour names in e-mail construction (drosophila -> D. melanogaster, latter parsed as. 'D. ').

adRn-s commented 2 weeks ago

something similar arose with BRB, I adjusted its INI file already... but I was not contempt with that solution.

ultimately, I strive to have a robust solution for all the 'end to end' passing (and parsing) of strings... from the UI to the pipeline(s).

at dissectBCL level, is the "mouse" string required for BRB and snakePipes? are these related? or is this issue a whole new problem (e.g. string is to be used by dissectBCL itself or multiqc)? In any case, maybe I can add a column to the Organism table and make the API used by our pipelines to respond with the snakePipes' version of organisms names. This way we accommodate both needs, user facing and 'computer' like names.

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