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cidgoh / pathogen-genomics-package

This is the DataHarmonizer spreadsheet web application bundled with pathogen genomics data entry and validation templates
MIT License
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MPX template: remove LIMS export field "PH_INSTRUMENT_CGN" #9

Closed griffie closed 1 year ago

griffie commented 1 year ago

In the CanCOGeN DH template, the sequencing instrument information is supposed to export to PH_INSTRUMENT_CGN field whereas the MPX template exports sequencing instrument to PH_INSTRUMENT.

For some reason both are showing up in the MPX export. Can we turn off the "PH_INSTRUMENT_CGN" field in the MPX export?

I'm not even sure how that field is showing up since it's not in the MPX template's LIMS export column at all...

ddooley commented 1 year ago

So the DataHarmonizer mapping for monkeypox shows that "sequencing instrument" for both canadian and international templates should export to PH_SEQUENCING_INSTRUMENT , which should get tacked onto end of fields. I can see previously there would have been an empty PH_INSTRUMENT_CGN field, and I have taken that out. I have ordered PH_SEQUENCING_INSTRUMENT to take its place.
This will be available on next release.