Running Scenic+ without Snakemake

[gilgolan73]

Hello,
I am encountering an issue with running Scenic+ using Snakemake (see issue #468), as instructed by the tutorial https://scenicplus.readthedocs.io/en/latest/human_cerebellum.html#Running-SCENIC+ .
Is there a possibility to run the rest of Scenic+ pipeline without Snakemake ? (but in a regular python code, as instructed by the old tutorial https://scenicplus.readthedocs.io/en/stable/pbmc_multiome_tutorial.html, or by another tutorial?).

Thank you,
Gil

[SeppeDeWinter]

Hi @gilgolan73

Yes, you can run the individual commands that are normally run within the Snakemake pipeline.
See: https://github.com/aertslab/scenicplus/blob/main/src/scenicplus/snakemake/Snakefile for more info.

Best,

Seppe