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hubmapconsortium / codex-pipeline

CODEX data processing code
GNU General Public License v3.0
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Update/fork to handle PhenoCycler (+Fusion) #45

Open mruffalo opened 1 year ago

mruffalo commented 1 year ago

The "CODEX v2" data layout significantly differs from what we've handled in the past. Using sample data from various groups, investigate what will need to be modified in our code to handle PhenoCycler data.

### Tasks
NickEngland commented 1 year ago

I've so far fixed the problem with running cwltool with singularity on the hive: https://github.com/hubmapconsortium/cwltool/pull/29 which was blocking me from testing the pipeline with the data.