This is a spatial transcriptomics analysis pipeline for Visium 10x platform. The pipeline is built in Snakemake and can be run on different platforms and high performance computing (HPC) systems.
The workflow expects Visum 10x samples under data folder in this format:
"data/{sample}/outs/filtered_feature_bc_matrix.h5"
This will register the directory name as sample name for later processing.
You can start the pipeline by calling,
snakemake -j 20
which will create a 20 threads job.