# 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 TBD ## Parameters ## Example Usage ## Containers ## Questions