SINCLAIR

SINgle CelL AnalysIs Resource

View the documentation here: https://ccbr.github.io/SINCLAIR/

Introduction

SINCLAIR 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.

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.

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Quickstart

SINCLAIR is available on biowulf with the ccbrpipeliner module as of release 8. You can load it on an interactive node with:

module load ccbrpipeliner/8

sinclair --help
sinclair --version

Example usage

1. Initialize your project

--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)

In /path/to/output/dir:

• assets/params.yml
• assets/input_manifest.csv
• assets/contrast_manifest.csv

3. Run the pipeline

A) preview without executing

sinclair run -preview --output /path/to/output/dir -params-file assets/params.yml

B) local run

sinclair run --output /path/to/output/dir -params-file assets/params.yml

C) submit to slurm

sinclair run --mode slurm --output /path/to/output/dir -params-file assets/params.yml

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 CCBR_Pipeliner@mail.nih.gov.