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AlexsLemonade / alsf-scpca

Management and analysis tools for ALSF Single-cell Pediatric Cancer Atlas data.
BSD 3-Clause "New" or "Revised" License
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Add entries for `ref_assembly` and `star_index` to `scpca-meta.json` files #177

Closed allyhawkins closed 8 months ago

allyhawkins commented 8 months ago

In working on processing projects through scpca-nf, I noticed that the libraries with multiplexing were not skipping genetic demuxing, even though the results files already exist and they should be skipped. When I went to look at why, it was because the scpca-meta.json for multiplexed samples did not contain a ref_assembly version. That's what we use to check to ensure we skip demultiplexing. Here, I'm updating the script we use to add in fields to the scpca-meta.json files to include the ref_assembly field.

When I was poking around, I also noticed that we don't store the star_index in scpca-meta.json for the multiplexed libraries, but we do for all other libraries. I am also adding that as a field to include in the json files here.

Note that I updated one of the json files and then re-ran the workflow and things were now skipping genetic demultiplexing as they should be.

allyhawkins commented 8 months ago

Just to check: are we setting this in the multiplexing workflow as we should?

Yes, we write out the meta object in the vireo process and the meta object should contain both of those items.