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Updating for test data

Open johnstonmj opened this issue 1 year ago • 0 comments

I was excited to try scRNA analysis through this Snakemake workflow, however, I encountered multiple errors trying to run the test dataset. I believe that I've corrected them here.

In brief:

  • Changing gene names from ABCDE to Abcde format.
  • Updating yaml for cellassign to allow tensorflow install.
  • Limiting threads for cellassign to 8 rather than 1000, as this would not dispatch on cluster.
  • Updating config to specify celltypes detected, as cell types with zero population cause errors.
  • Added warning message to scripts/common.R to notify when a zero population cell type is encountered.
  • Reduced minimum cell count required for clustering, as this was causing the test dataset to fail.

Hope this helps!

johnstonmj avatar Nov 22 '22 04:11 johnstonmj