single-cell-rna-seq
single-cell-rna-seq copied to clipboard
Updating for test data
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!