nf-core/epitopeprediction

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Introduction

nf-core/epitopeprediction is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation.

Pipeline steps

• Input
• Transcripts
• Prediction

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

i. Install nextflow

ii. Install one of docker, singularity or conda

iii. 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.

iv. Start running your own analysis!

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

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

Documentation

The nf-core/epitopeprediction pipeline comes with documentation about the pipeline, found in the docs/ directory:

1. Installation
2. Pipeline configuration
   • Local installation
   • Adding your own system config
   • Reference genomes
3. Running the pipeline
4. Output and how to interpret the results
5. Troubleshooting

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 Slack (you can join with this invite).

Citation

nf-core/epitopeprediction was originally written by Christopher Mohr and Alexander Peltzer.

You can cite the nf-core pre-print as follows:

Ewels PA, Peltzer A, Fillinger S, Alneberg JA, Patel H, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. nf-core: Community curated bioinformatics pipelines. bioRxiv. 2019. p. 610741. doi: 10.1101/610741.