Snakemake pipeline for 10x Genomics Multiome outputs

[keller-mark]

We should aim to have tutorials / examples for how to visualize data from the most-commonly used sequencing instruments and their associated data processing pipelines.

One of these instruments / experiment types is 10x Genomics Multiome: https://www.10xgenomics.com/products/single-cell-multiome-atac-plus-gene-expression

We should develop a Snakemake pipeline which:

1. Downloads an example Multiome dataset from https://www.10xgenomics.com/resources/datasets?query=&page=1&configure%5BhitsPerPage%5D=50&configure%5BmaxValuesPerFacet%5D=1000&refinementList%5Bproduct.name%5D%5B0%5D=Single%20Cell%20Multiome%20ATAC%20%2B%20Gene%20Expression , for example https://www.10xgenomics.com/resources/datasets/10-k-human-pbm-cs-multiome-v-1-0-chromium-x-1-standard-2-0-0
2. Uses the Muon package to read the 10x-formatted HDF5 files into MuData objects https://muon.readthedocs.io/en/latest/io/input.html#count-matrices
3. Configures Vitessce to visualize this dataset https://github.com/vitessce/paper-figures/blob/main/multiome/src/multiome.ipynb