running integration metric through scib-pipeline

[olhakholod]

Hello!

I have integrated two tissues via Seurat integration pipeline. I would like to use scib-pipeline to evaluate the quality of this integration.

I have converted Seurat object to anndata and tried to run the pipeline via this script:

snakemake --configfile configs/test_data-R4.0.yaml --cores 1

However, the pipeline asked me to preprocess and integrate data again. I was wondering if I misinterpret some steps of the pipeline and I would not be able to output metric for integrated data from Seurat.

Thank you for your help!
Olha