README.md

# Cellranger count

This is an Astrocyte workflow to run Cellranger count to generate cell-by-gene matrices from fastq files generated from 10x Genomics scRNA sequencing runs.

# To-do:

- Modify main.nf to run the script appropriately
- Include parameter options (introns, expect cells, etc)
- Compare to GHH version
- Provide option to also run cellbender
- Complete this document
- Copy this content to index.md
- Remove vizapp directory if unnecessary
- Populate test_data with PBMC2k
- update astrocyte_pkg.yml

## The Workflow


## Parameters


## Example Usage


## Containers


## Questions