ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

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Introduction

ViroProfiler is a bioinformatics best-practice analysis pipeline for viral metagenomics data analyses.

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.

Quick Start

1. Install Nextflow (>=21.10.3)

2. Install Singularity (you can follow this tutorial) or Docker. Other Podman, Shifter or Charliecloud for full pipeline reproducibility. However, only Docker and Singularity were tested. (you can use Conda/Mamba 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 database.

   nextflow run deng-lab/viroprofiler -profile <YOURPROFILE>
   
   # ex.
   # nextflow run deng-lab/viroprofiler -profile singularity

   By default, database will be downloaded to the $HOME/viroprofiler directory. You can change database path using the --db parameter. For example, if you want to download the database to /db/path directory, you can run the pipeline as follows:

   nextflow run deng-lab/viroprofiler -profile <YOURPROFILE> --db /db/path

   • If you are using Singularity, please set 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.
   • If you are using Docker, please replace the profile with docker: -profile docker.

4. Test the pipeline on a minimal dataset,

   nextflow run deng-lab/viroprofiler -profile test,<YOURPROFILE>
   
   # ex.
   # nextflow run deng-lab/viroprofiler -profile test,singularity

   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, singularity, podman, shifter, charliecloud and conda which instruct the pipeline to use the named tool for software management. For example, -profile test,docker.
   • 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.

5. Start running your own analysis!

   You may create a config file to customize the parameters of the pipeline and use -c to load the config. Please check custom.config for an example.

   You can also specify the parameters in a file and use -params-file to load the parameters. Please check params.yml for an example.

   nextflow run deng-lab/viroprofiler --input samplesheet.csv -c custom.config -params-file params.yml -profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
   
   # ex.
   # nextflow run deng-lab/viroprofiler --input samplesheet.csv -c custom.config -params-file params.yml -profile slurm,singularity

Updating the pipeline

nextflow pull deng-lab/viroprofiler

Documentation

Please refer to the documentation page.

Credits

ViroProfiler was originally written by Jinlong Ru.

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

• ...

Contributions and Support

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

For further information or help, please open an issue.

Citations

If you use ViroProfiler for your analysis, please cite the publication as follows:

ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng

[journal]

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

This pipeline uses code and infrastructure developed and maintained by the nf-core initative, and reused here under the MIT license. 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.