nf-core/epitopeprediction is a bioinformatics best-practice analysis pipeline for epitope prediction and annotation.
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.
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 institutein your command. This will enable either
singularityand 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.
The nf-core/epitopeprediction pipeline comes with documentation about the pipeline, found in the
- Pipeline configuration
- Running the pipeline
- Output and how to interpret the results
If you would like to contribute to this pipeline, please see the contributing guidelines.
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.