nf-core/epitopeprediction is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation. The pipeline performs epitope predictions for a given set of variants or peptides directly using state of the art prediction tools. Additionally, resulting prediction results can be annotated with metadata.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible.

Quick Start

  1. Install nextflow

  2. Install either Docker or Singularity for full pipeline reproducibility (please only use Conda as a last resort; see docs)

  3. Download the pipeline and test it on a minimal dataset with a single command:

    nextflow run nf-core/epitopeprediction -profile test,<docker/singularity/conda/institute>

    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.

  4. Start running your own analysis!

    nextflow run nf-core/epitopeprediction -profile <docker/singularity/conda/institute> --input '*.vcf.gz' --genome GRCh37

See usage docs for all of the available options when running the pipeline.


The nf-core/epitopeprediction pipeline comes with documentation about the pipeline which you can read at


nf-core/epitopeprediction was originally written by Christopher Mohr from Institute for Translational Bioinformatics and Quantitative Biology Center and Alexander Peltzer from Böhringer Ingelheim. Further contributions were made by Sabrina Krakau from Quantitative Biology Center.

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 #epitopeprediction channel (you can join with this invite).


If you use nf-core/epitopeprediction for your analysis, please cite it using the following doi: 10.5281/zenodo.3564666

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. ReadCube: Full Access Link