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https://github.com/mskcc/vepcheck

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

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Nextflow pipeline to check different vep version

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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).