SINCLAIR

SINgle CelL AnalysIs Resource

Table of contents

• 1. Introduction
• 2. Overview
• 3. Documentation
• 4. Feedback

1. Introduction

The SINCLAIR - SINgle CelL AnalysIs Resource was developed by the CCR Collaborative Bioinformatics Resource as an open-source, reproducible solution for multiple single cell next-generation modalities. It has been developed solely on Biowulf using Nextflow.

2. Overview

The pipeline currently begins with either sample FASTQ file or h5 Aligned reads, completing per sample quality control, and per-contrast integration. Quality control reports are generated, as are per-contrast integration reports.

^{Overview of Single Cell RNASeq Gene Expression Pipeline}

3. Basic Deployment

Usage

sinclair --help
sinclair --version

Example workflow

# 1) run initialization
mkdir -p /path/to/output/dir
cd /path/to/output/dir
sinclair init

# 2) update the config files as needed
## can change whether cellranger is deployed, species, names of manifest files (default locations listed below)
/path/to/output/dirnextflow.config
/path/to/output/dir/assets/contrast_manifest.csv /path/to/output/dir/assets/input_manifest.csv

# 3) deploy the pipeline
## A) STUBRUN
sinclair run -stub -entry GEX

## B) local run
sinclair run -entry GEX

## C) submit to slurm
sinclair run --mode slurm -entry GEX

# 4) OPTIONAL resume
sinclair run --mode slurm -entry GEX -resume

4. Detailed Documentation

Please view the repositories documentation for full details on deploying the pipeline, features, testing, and expected outputs.

5. Feedback

For comments/suggestions/advice please reach out to Samantha Chill or Nathan Wong.