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 7.1.0 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

- Fastq: The fastq files for the sample. Regardless of the files that are
selected, only those matching the sample name will be included.

- sample_sheet: This is a file with the following named columns:

    - **sample**: The name of the sample. This must match the prefix of the associated fastq files.
    - **reference**: Which reference genome to use. This workflow currently supports the values "hg38", "mm10", or "barnyard" (hg38 and mm10 combined).
    - **expectCells**: The number of cells expected from this sample. Set to "auto" for auto-detection (recommended).
    - **chemistry**: The chemistry used to generate libraries. Set to "auto" for auto-detection 
    (recommended). Note that if the chemistry is 3' v1 or you're analyzing GEX data alone generated from 
    multiome, you must set this explicitly. Possible values:
        - "auto": auto detect
        - "SC3Pv1": Single cell 3' v1
        - "SC3Pv2": Single cell 3' v2
        - "SC3Pv3": Single cell 3' v3
        - "SC3Pv3LT": Single cell 3' v3 LT
        - "SC3Pv3HT": Single cell 3' v3 HT
        - "SC5P-PE": Single cell 5' paired-end
        - "SC5P-R2": Single cell 5' R2-only
        - "ARC-v1": GEX only from multiome
    - **introns**: true/false. Whether to count intronic reads.
    - **noBam**: true/false. Whether to skip bam file generation. This will save some time and space, but
      bam files may be required for downstream analysis and/or deposition into public databases.
      
## Questions

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