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VEuPathDB / EdaNewIssues

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VDI Mbio: Expand user upload options to include tsv + metadata #647

Open asizemore opened 1 year ago

asizemore commented 1 year ago

Currently the mbio upload form allows biom files only. @dpbisme mentioned this is not ideal, because biom files are tough to make for the general user. Users are much more likely to have tsv files: one for the taxa abundance and one for the sample metadata.

We can be very specific about what we expect such a file pair to look like in terms of row names of one are the column names of the other, for example.

This feature is also likely to become increasingly relevant as we (hopefully) connect wiht czid and begin to get metagenomic data from nephele.

dmfalke commented 1 year ago

I'm not sure which repo this belongs in. I think only the dataset handler would have to be updated, to expand file types. It's also possible that VDI will be in place, by the time we get to this.