README.md

# Cellranger count Astrocyte pipeline

## Introduction

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.
Like other Astrocyte workflows, this workflow uses Nextflow, a bioinformatics
workflow and pipeline development tool. 

This workflow runs cellranger version 7.0.1 using user provided fastq files
derived from single cell sequencing data using the 10x Genomics platform. 
Output are standard cellranger outputs, including a cell-by-gene matrix in 
both MTX and h5 formats, a summary of the run in an HTML output, and a BAM
file of aligned reads. These outputs can then be used for downstream analysis.

## Parameters

- Sample: The name of the sample. This should match the sample 
name of the fastq files.
- Fastq: The fastq files for the sample. Regardless of the files that are
selected, only those matching the sample name will be included.
- Reference: Which reference genome to use. Current choices are 
hg38 and mm10.
- expectCells: How many cells are expected to be present. Leave at 
the default (0) to automatically estimate. This may be manually set if
the estimate is inaccurate.
- Chemistry: The chemistry used to create the library. Automatic detection
is recommended, but if the library chemistry is **3'v1** or **multiome GEX**, 
you must set these manually.
- Introns: Should intronic reads be counted? Recommended to 
keep true. Note that this **must** be true to process data from single nucleus
suspensions.
- noBam: Should the pipeline skip generating a bam file?
Bam file generation is recommended, but it may be skipped to reduce file 
size output and speed up processing time.

## Questions

Please reach out to the workflow maintainer (john.lafin@utsouthwestern.edu)
with any questions.