From 21c4e874ea89534309d9e3de8112f123bbfac7cc Mon Sep 17 00:00:00 2001
From: "Gervaise H. Henry" <gervaise.henry@utsouthwestern.edu>
Date: Fri, 8 Jun 2018 11:47:58 -0500
Subject: [PATCH] Update README.md

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 README.md | 13 ++++++++++++-
 1 file changed, 12 insertions(+), 1 deletion(-)

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-# CellRanger Pipeline
+10x Genomics scRNA-Seq (cellranger) mkfastq Pipeline
+========================================
 
+Introduction
+------------
+
+This pipeline is a wrapper for the cellranger mkfastq tool from 10x Genomics, which is a wrapper for Illumina's bcl2fastq tool. It takes tarballed bcl files from 10x Genomics Single Cell Gene Expression libraries, and untar's and deconvolves them into fastq's.
+
+The pipeline uses Nextflow, a bioinformatics workflow tool.
+
+This pipeline is primarily used with a SLURM cluster on the BioHPC Cluster. However, the pipeline should be able to run on any system that Nextflow supports.
+
+Additionally, the pipeline is designed to work with Astrocyte Workflow System using a simple web interface.
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