This directory contains integrations tests for ScanNeo2. Here, we provide a set of configuration files and expected output files that can be used to test the installation of ScanNeo2.

Here, we provide folders for a set of different test cases.

In custom-test we call ScanNeo2 using a set of pre-calculated SNVs (data/variants/snvs.vcf) using provided mhc-I alleles (data/hla/mhc-I.tsv). In addition, the expected output is stored in results.

In indel-test we call ScanNeo2 to detect indel-derived neoantigens using provided mhc-I alleles (data/hla/mhc-I.tsv). The exptected output is stored in results.

snakemake --cores all --configfile .tests/integration/<testcase>/config/config.yml

The expected output is stored in the results folder in the root directory of ScanNeo2.