https://github.com/mskcc/vepcheck

Nextflow pipeline to check different vep version
https://github.com/mskcc/vepcheck

Last synced: 4 months ago
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Nextflow pipeline to check different vep version

• Host: GitHub
• URL: https://github.com/mskcc/vepcheck
• Owner: mskcc
• License: mit
• Created: 2024-07-09T14:36:23.000Z (almost 2 years ago)
• Default Branch: master
• Last Pushed: 2024-11-04T23:33:25.000Z (over 1 year ago)
• Last Synced: 2025-11-23T04:04:02.165Z (7 months ago)
• Language: Nextflow
• Size: 905 KB
• Stars: 0
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: .github/CONTRIBUTING.md
  • License: LICENSE
  • Citation: CITATIONS.md

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README

          
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## Introduction

**mskcc/vepcheck** is a bioinformatics pipeline that compares the annotation differences across different annotation pipelines. It looks at differences in vep versions as well as differences in the vcf2maf and vcf2maf-light convertors.

![Workflow Diagram](assets/pipeline.png)

## Usage

> [!NOTE]

> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.

Now, you can run the pipeline using:

```bash

nextflow run mskcc/vepcheck \

   -profile  \

   --input samplesheet.csv \

   --outdir 

```

> [!WARNING]

> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_;

> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files).

## Credits

mskcc/vepcheck was originally written by nikhil.

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](.github/CONTRIBUTING.md).

## Citations

An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.

This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/master/LICENSE).

> **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](https://dx.doi.org/10.1038/s41587-020-0439-x).