MHC2-prediction-workflows

A Nextflow script using MixMHC2pred (https://github.com/GfellerLab/MixMHC2pred) to predict MHC class II ligands and epitopes given a protein FASTA file and the desired alleles.

Setup

You need Nextflow (>=24.04.0) and docker installed.

Before the first execution run the Makefile in the main directory by executing

main

in the root filder of the project. This should download respectively build all required docker images.

Running the workflow

After downloading and building the images, execute the script like:

nextflow run main.nf -profile docker \
    --fasta /path/to/proteins.fasta  \
    --pep_length_min 12  --pep_length_max 15 \
    --alleles "DRB1_15_01 DRB5_01_01"

For the alleles, please refer to the MixMHC2pred homepage (https://github.com/GfellerLab/MixMHC2pred)

The output of the prediction will be given in the results folder.

Arguments

name	description	default
--fasta	path to the FASTA file containing protein sequences
--pep_length_min	Minimal length of peptides for the prediction	15
--pep_length_max	Directory where results should be stored	15
--alleles	Set to false if there are decoys in your FASTA file	"DRB1_15_01 DRB5_01_01"