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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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Update alevin-fry images to 0.4.1 (and maybe salmon?) #118

Closed jashapiro closed 3 years ago

jashapiro commented 3 years ago

In response to some comments from us https://github.com/COMBINE-lab/alevin-fry/issues/22#issuecomment-885195051 alevin-fry now has better .json output files, so we should update. When we do that, some of the output files will change, but for the better! However, this will temporarily break scpcaTools (filing that issue separately).

We may want to wait for a coming version bump for salmon that will come in parallel, which adds back the cmd_info.json file for --rad outputs.

One other note along with that is that we can remove the t2g file (--tgMap) from the salmon alevin call, as this is no longer needed with --rad