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A containerized bioinformatics pipeline for viral metagenomic data analysis

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# ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis

[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A521.10.3-23aa62.svg)](https://www.nextflow.io/)
[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?logo=docker)](https://www.docker.com/)
[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg)](https://sylabs.io/docs/)
[![DOI](https://zenodo.org/badge/537899739.svg)](https://zenodo.org/badge/latestdoi/537899739)

```
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    `888.8'     88   88     88   88    _||_     88     88   88  88     88   88  888ooo88  88
     `888'      88   88     88   88  // || \\   88     88   88  88     88   88  88    .o  88
      `8'      o88o o88b     o888o  //      \\ d88b     o888o  o88o   o88o o88o `Y8bd8P' 088b

```

## Introduction

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

The pipeline is built using [Nextflow](https://www.nextflow.io), 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.

![viroprofiler workflow](https://raw.githubusercontent.com/deng-lab/viroprofiler/main/docs/images/viroprofiler.png)

## Quick Start

1. Install one of the supported container engines using **root** privileges:

- [Singularity](https://sylabs.io/guides/3.0/user-guide/quick_start.html#quick-installation-steps)
   - [Charliecloud](https://hpc.github.io/charliecloud/install.html)
   - [Docker](https://docs.docker.com/install/)
   - [Podman](https://podman.io/getting-started/installation)
   - [Shifter](https://github.com/NERSC/shifter)

2. Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html).

3. Install Nextflow using conda:

```bash
   # You may need to restart your terminal before running the following commands
   conda install -c bioconda nextflow
   ```

4. Download the pipeline and database.

```bash
   # setup database
   nextflow run deng-lab/viroprofiler -r main -profile singularity --mode "setup"
   ```

`-profile` specifies the container engine to use. You can use `singularity`, `charliecloud`, `docker`, `podman`, or `shifter`. You can also use `test` to run the pipeline with test data after setting up the database.

5. Run the pipeline,

```bash
   # run test
   nextflow run deng-lab/viroprofiler -r main -profile singularity,test

# run your own data
   nextflow run deng-lab/viroprofiler -r main -profile singularity --input samplesheet.csv
   ```

6. Update the pipeline,

```bash
   nextflow pull deng-lab/viroprofiler
   ```

Please refer to the [tutorial](https://deng-lab.github.io/viroprofiler/tutorial) for more information on how to run the pipeline with customized parameters and options.

## Documentation

Please refer to the [documentation](https://deng-lab.github.io/viroprofiler).

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).

For further information or help, please [open an issue](https://github.com/deng-lab/viroprofiler/issues).

## Citations

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

> *Jinlong Ru, Mohammadali Khan Mirzaei, Jinling Xue, Xue Peng, Li Deng*. **ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis**. *Gut Microbes* (2023); doi: https://doi.org/10.1080/19490976.2023.2192522

An extensive list of references for the tools and data used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. If you use ViroProfiler for your work, please cite the relevant references.

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