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mskcc/neoantigenpipeline\n\n[![GitHub Actions CI Status](https://github.com/mskcc/neoantigenpipeline/actions/workflows/ci.yml/badge.svg)](https://github.com/mskcc/neoantigenpipeline/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/mskcc/neoantigenpipeline/actions/workflows/linting.yml/badge.svg)](https://github.com/mskcc/neoantigenpipeline/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.0-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000\u0026logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000\u0026logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/mskcc/neoantigenpipeline)\n\n## Introduction\n\n**mskcc/neoantigenpipeline** is a bioinformatics pipeline that adapts Luksza et al.'s neoantigenEditing and fitness pipeline for usage by investigators in MSK. The pipeline curently supports working with TEMPO output mafs, Facets gene-level copy number calls, and Polysolver outputs. It outputs a json representation of the clonal structure of the tumor annotated with neoantigen burden, driver burden, and fitness of the clone. Also individual neoantigens are labeled with the quality of the neoantigen as described by Luksza et al.\n\n![Workflow Diagram](assets/workflow_diagram.png)\n\n\n1. Create phylogenetic trees using [PhyloWGS](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0602-8)\n2. Use [netMHCpan-4](https://services.healthtech.dtu.dk/services/NetMHCpan-4.1/) to calculate binding affinities \n3. Use [netMHCpanStab](https://services.healthtech.dtu.dk/services/NetMHCstabpan-1.0/) to calculate stability scores \n4. Use Luksza et al.'s neoantigen quality and fitness computations tool ([NeoantigenEditing](https://github.com/LukszaLab/NeoantigenEditing)) to evaluate peptides\n\n## Usage\n\n\u003e [!NOTE]\n\u003e If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,maf,facets_hisens_cncf,hla_file\ntumor_normal,temp_test_somatic_unfiltered.maf,facets_hisens.cncf.txt,winners.hla.txt\ntumor_normal2,temp_test_somatic_unfiltered.maf,facets_hisens.cncf.txt,winners.hla.txt\n```\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run mskcc/neoantigenpipeline \\\n   -profile prod,\u003cdocker/singularity\u003e \\\n   --input samplesheet.csv \\\n   --outdir \u003cOUTDIR\u003e\n```\n\n\u003e [!WARNING]\n\u003e Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\n## Credits\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n - Nikhil ([@nikhil](https://github.com/nikhil))\n - John ([@johnoooh](https://github.com/johnoooh))\n - Alex ([@pintoa1-mskcc](https://github.com/pintoa1-mskcc))\n - Martina ([@BradicM](https://github.com/BradicM))\n - Allison ([@arichards2564](https://github.com/arichards2564))\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\n## Citations\n\n\n- Deshwar, A. G., Vembu, S., Yung, C. K., Jang, G. H., Stein, L., \u0026 Morris, Q. (2015). PhyloWGS: reconstructing subclonal composition and evolution from whole-genome sequencing of tumors. Genome biology, 16(1), 35. https://doi.org/10.1186/s13059-015-0602-8\n- Jurtz, V., Paul, S., Andreatta, M., Marcatili, P., Peters, B., \u0026 Nielsen, M. (2017). NetMHCpan-4.0: Improved Peptide-MHC Class I Interaction Predictions Integrating Eluted Ligand and Peptide Binding Affinity Data. Journal of immunology (Baltimore, Md. : 1950), 199(9), 3360–3368. https://doi.org/10.4049/jimmunol.1700893\n- Łuksza, M., Sethna, Z.M., Rojas, L.A. et al. Neoantigen quality predicts immunoediting in survivors of pancreatic cancer. Nature 606, 389–395 (2022). https://doi.org/10.1038/s41586-022-04735-9\n- Rasmussen, M., Fenoy, E., Harndahl, M., Kristensen, A. B., Nielsen, I. K., Nielsen, M., \u0026 Buus, S. (2016). Pan-Specific Prediction of Peptide-MHC Class I Complex Stability, a Correlate of T Cell Immunogenicity. Journal of immunology (Baltimore, Md. : 1950), 197(4), 1517–1524. https://doi.org/10.4049/jimmunol.1600582\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nThis pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE).\n\n\u003e **The nf-core framework for community-curated bioinformatics pipelines.**\n\u003e\n\u003e Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso \u0026 Sven Nahnsen.\n\u003e\n\u003e _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fneoantigen-pipeline","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fmskcc%2Fneoantigen-pipeline","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fmskcc%2Fneoantigen-pipeline/lists"}