Introduction

The GRiPHin pipeline currently takes either a samplesheet (nf-core style) or a directory with PHoeNIx style output.

DHQP/griphin is a bioinformatics best-practice analysis pipeline for A pipeline to convert PHoeNIx output into a custom report.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Pipeline summary

Quick Start

1. Install Nextflow (>=21.10.3)

2. Install any of Docker, Singularity (you can follow this tutorial), for full pipeline reproducibility (you can use Conda both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see docs).

3. Download the pipeline and run with a single command:

   nextflow run nf-core/griphin -profile singularity --outdir <OUTDIR> --input samplesheet.csv

   Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (YOURPROFILE in the example command above). You can chain multiple config profiles in a comma-separated string.

   • The pipeline comes with config profiles called docker and singularity which instruct the pipeline to use the named tool for software management. For example, -profile docker.
   • If you are using singularity, please use the nf-core download command to download images first, before running the pipeline. Setting the NXF_SINGULARITY_CACHEDIR or singularity.cacheDir Nextflow options enables you to store and re-use the images from a central location for future pipeline runs.

4. Start running your own analysis!

   nextflow run DHQP/griphin --input samplesheet.csv --outdir <OUTDIR> -profile <docker/singularity>

Credits

DHQP/griphin was originally written by Jill Hagey.

We thank the following people for their extensive assistance in the development of this pipeline:

• Maria Diaz @MzDiaz824
• Nick Vlachos @nvlachos
• Thao Masters @masters-thao
• Alyssa Kent @Alyssa-Kent

Contributions and Support

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

For further information or help, don't hesitate to get in touch on the Slack #griphin channel (you can join with this invite).

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

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.

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