Introduction
============

LENS
____

The Landscape of Effective Neoantigens Software (LENS) is a tumor antigen
discovery workflow. Tumor antigens serve as potential therapeutic targets for
tumor elimination by a patient's immune system. The immune system is primed to
target these tumor antigens through vaccination. More infromation on
therapeutic cancer vaccines can be found in `Therapeutic cancer vaccines:
advancements, challenges and prospects
<https://www.nature.com/articles/s41392-023-01674-3>`_ (Fan et al., 2023).


LENS currently provides predicted peptide-MHCs (pMHCs)
from:

 - Somatic Nucleotide Variants (SNVs)
 - Somatic Insertion and Deletion Variants (InDels)
 - Splice Variants
 - Fusion Events
 - Endogenous Retroviruses (ERVs)
 - Viruses
 - Cancer-testis Antigens (CTAs)

Running LENS
____________

LENS runs within RAFT, a Nextflow-based workflow manager that ensures running
the workflow is a smooth process. We touch on RAFT within this tutorial, but we
encourage users to further explore the `RAFT documentation
<https://reproducible-analyses-framework-and-tools.readthedocs.io/en/latest/>`_.
The :doc:`installing_raft` section contains more information on install RAFT
prior to running LENS.

A demonstration version of LENS is available for users that do not have their
own samples or are interested in learning more about how LENS works.

Sample Prerequisites
____________________

LENS can be run on multiple patients simultaneously and there are benefits to
running multiple patients (such as shared tumor splice variant detection with
``SNAF`` and improved CNA detection with ``CNVKit``, but only one patient worth
of samples is required.

It is strongly recommended to run LENS with the following sample types (per patient):
 - DNA tumor
 - DNA normal
 - RNA tumor

Additionally, users should provide a tissue-matched normal RNA
sample (e.g. GTEx or `Fagerberg et al., 2014 <https://www.mcponline.org/article/S1535-9476(20)34633-8/fulltext>`_).

.. image::
   patient_names_and_runs.png
   :width: 675