qbic-pipelines/cellranger

Nextflow wrapper around the Cell Ranger pipeline for single cell RNAseq analysis.

Introduction

qbic-pipelines/cellranger is a Nextflow pipeline that wraps the Cell Ranger pipeline for single cell RNAseq analysis. It additionally performs QC on the Fastq files with FastQC and summarizes the QC with MultiQC.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

1. Install nextflow (>=20.10.0)

2. Install any of Docker, Singularity, Podman, Shifter or Charliecloud for full pipeline reproducibility (please only use Conda as a last resort; see docs)

3. Download the pipeline and test it on a minimal dataset with a single command:

   nextflow run qbic-pipelines/cellranger -profile test,<docker/singularity/podman/conda/institute>

   Please check nf-core/configs to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use -profile <institute> in your command. This will enable either docker or singularity and set the appropriate execution settings for your local compute environment.

4. Start running your own analysis!

   nextflow run qbic-pipelines/cellranger -profile <docker/singularity/podman/conda/institute> --input 'samplesheet.tsv' --genome GRCh38

See usage docs for all of the available options when running the pipeline.

Updating the pipeline container and making a new release

Cell Ranger is a commercial tool and cannot be distributed. Updating the Cell Ranger version in the container and pushing the update to Dockerhub needs needs to be done manually.

1. Clone this pipeline repository. E.g. with the gh GitHub cli:

   gh repo clone qbic-pipelines/cellranger
   cd cellranger

2. Navigate to the Cell Ranger download page and download the tar ball of the desired Cell Ranger version with curl or wget. Place this file inside the recently cloned pipeline directory.

3. Edit the Dockerfile: update the Cell Ranger version in this line.

   ENV CELLRANGER_VER <VERSION>

4. Create the container:

   docker build . -t qbicpipelines/cellranger:dev
   docker push qbicpipelines/cellranger:dev

5. If preparing for new release: bump to the desired pipeline version (<version>) and container tag (same as pipeline version) in the main.nf manifest, nextflow.config container definition, and ci.yml GitHub actions workflow. Then push the latest and release container tags.

   docker pull qbicpipelines/cellranger:dev
   docker tag qbicpipelines/cellranger:dev qbicpipelines/cellranger:latest
   docker push qbicpipelines/cellranger:latest
   docker tag qbicpipelines/cellranger:latest qbicpipelines/cellranger:<version>
   docker push qbicpipelines/cellranger:<version>

Pipeline Summary

By default, the pipeline currently performs the following:

• Sequencing quality control (FastQC)
• single-cell data analysis with Cell Ranger (cellranger count)
• Overall pipeline run summaries (MultiQC)

Documentation

The qbic-pipelines/cellranger pipeline comes with documentation about the pipeline: usage and output.

Credits

qbic-pipelines/cellranger was originally written by Gisela Gabernet.

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

This pipeline was created with the nf-core template. You can cite the nf-core publication as follows:

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.

In addition, references of tools and data used in this pipeline are as follows: