nextflow_pvacseq

Introduction

nextflow_pvacseq is a custom Nextflow pipeline that transforms MAF files into VCF, annotates them with VEP, and analyzes them with pVACseq to facilitate the investigation of tumor neoantigens. It supports inputs in both MAF and VCF formats.

Pipeline Summary

The pipeline performs the following steps:

1. Input Preprocessing

   • Accepts MAF or VCF files as input.

   • Converts MAF to VCF (if required) using maf2vcf.

2. Variant Annotation

   • Annotates variants using VEP, configured for pVACseq requirements.

3. Loading HLA

   • Reads and processes HLA typing information from a user-provided CSV file.

4. pVACseq Setup

   • Configures and downloads MHC class I and II reference files required by pVACseq if not provided.

5. pVACseq Execution

   • Runs pVACseq to predict tumor neoantigens.

6. MultiQC

   • Aggregates results with MultiQC.

Usage

Required Inputs

1. Input Files

   • A directory containing *.maf or *.vcf files.

2. HLA Typing Information

   • A CSV file (--hla_csv) in the format:

     Sample_ID,HLA_Types
     TCGA-G4-6310-01A-11D-1719-10,HLA-C05:01;HLA-C06:02;HLA-B45:01;HLA-A29:02;HLA-B44:02;HLA-A02:01
     

3. Reference Genome

   • A FASTA file (--fasta).

4. VEP Requirements (Optional)

   • Pre-downloaded VEP cache (--vep_cache) and/or VEP plugins (--vep_plugins).

   • If not provided, the pipeline will download the required files automatically.

5. pVACseq Requirements (Optional)

   • Pre-installed IEDB directory (--pvacseq_iedb).

   • If not provided, the pipeline will download and configure IEDB automatically.

Running the Pipeline

nextflow run main.nf \
   -profile <docker|conda> \
   --input <INPUT DIRECTORY> \
   --hla_csv <HLA CSV FILE> \
   --fasta <REFERENCE FASTA> \
   --outdir <OUTPUT DIRECTORY>

Testing the Pipeline

A minimal test dataset is included with the pipeline to verify that installation and execution work correctly. The test profile uses online VEP annotation, so no local VEP cache is required.

⚠️ This mode is intended only for testing. It is not recommended for real analyses, as online VEP annotation is slower and less reproducible.

nextflow run main.nf -profile test,<docker|conda>

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

• pVACseq

Jasreet Hundal+, Susanna Kiwala+, Joshua McMichael, Christopher A Miller, Alexander T Wollam, Huiming Xia, Connor J Liu, Sidi Zhao, Yang-Yang Feng, Aaron P Graubert, Amber Z Wollam, Jonas Neichin, Megan Neveau, Jason Walker, William E Gillanders, Elaine R Mardis, Obi L Griffith, Malachi Griffith. pVACtools: a computational toolkit to select and visualize cancer neoantigens. Cancer Immunology Research. 2020 Mar;8(3):409-420. DOI: 10.1158/2326-6066.CIR-19-0401. PMID: 31907209. (+) equal contribution.

Jasreet Hundal, Susanna Kiwala, Yang-Yang Feng, Connor J. Liu, Ramaswamy Govindan, William C. Chapman, Ravindra Uppaluri, S. Joshua Swamidass, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. Accounting for proximal variants improves neoantigen prediction. Nature Genetics. 2018, DOI: 10.1038/s41588-018-0283-9. PMID: 30510237.

Jasreet Hundal, Beatriz M. Carreno, Allegra A. Petti, Gerald P. Linette, Obi L. Griffith, Elaine R. Mardis, and Malachi Griffith. pVACseq: A genome-guided in silico approach to identifying tumor neoantigens. Genome Medicine. 2016, 8:11, DOI: 10.1186/s13073-016-0264-5. PMID: 26825632.

• VEP

McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology Jun 6;17(1):122. (2016) doi:10.1186/s13059-016-0974-4

• vcf2maf

Cyriac Kandoth. mskcc/vcf2maf: vcf2maf v1.6. (2020). doi:10.5281/zenodo.593251

• nf-core template

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.