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
# --output is optional and defaults to your current working directory.
sinclair init --output /path/to/output/dir

# 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/dir/nextflow.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 --output /path/to/output/dir

## B) local run
sinclair run -entry GEX --output /path/to/output/dir

## C) submit to slurm
sinclair run --mode slurm -entry GEX --output /path/to/output/dir

# 4) OPTIONAL resume
sinclair run --mode slurm -entry GEX -resume --output /path/to/output/dir

4. Detailed Documentation

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

Help & Contributing

Come across a bug? Open an issue and include a minimal reproducible example.

Have a question? Ask it in discussions.

Want to contribute to this project? Check out the contributing guidelines.

General Inquiries and Collaboration: Please contact the CCBR Pipeliner team at [email protected].