Repo with workflows for generating azimuth reference objects.

This repository contains the Dockerfile and snakemake workflows that are used to generate the azimuth references that are hosted online. Each reference directory contains a Snakefile and associated scripts that can be run to regenerate each reference (and associated demo data) from publicly available download links of the underlying data. To run:

snakemake --use-singularity --cores 1 all

The Azimuth package provides the AzimuthReference function to facilitate converting existing Seurat objects into the specific format expected by Azimuth. Details on the required reference format can be viewed here. For examples starting with a Seurat object, see the export.R scripts in the workflows in this repo (e.g. human pancreas).