nf-hlamajority: An Automated Nextflow Pipeline for Consensus HLA Genotyping in Neoantigen Prediction Workflows
Code to generate figures from application note for nf-hlamajority
Upload outputs of nf-hlamajority to Zenodo and add scripts to download them
To regenerate the figures from the submitted version of the paper (submitted 01/06/2026):
Clone the repository specifying the branch
git clone --recurse-submodules --branch v1.2.0 https://github.com/kevinpryan/hlamajority-appnote.git
Run bash download-data.sh to download the nf-hlamajority output data from Zenodo (2.4 GB)
Run bash run-all-app-note-thesis.sh to run the downstream processing and generate the figures from the app note and the thesis chapter
Requirements:
- docker
- nextflow
You will find app note Figures 1D,E combined at results/app_note/plots/hlamajority-1000genomes-nci-combined-20260529.svg, and the supplementary figure at results/app_note/plots/hlamajority-1000genomes-wgs.svg.
Run the Docker images containing all dependencies to run Rscripts as follows:
bash launch-container.sh
and go to http://localhost:8787/ on any web browser to open Rstudio, open the directory /hlamajority-paper/