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Scanneo2 is a snakemake workflow for detecting neoantigens from multiple sources. These include alternative splicing, exitron splicing, gene fusion, indels, and SNVs.
Scanneo2 requires snakemake and snakedeploy which are most easily installed using the Mamba Package Manager (or by conda itself). If neither mamba nor conda is present, it is best to install it from Mambaforge. We provide an environment.yml which allows creating a mamba directory that includes the above-defined dependencies.
Simply, run
mamba env create --file https://raw.githubusercontent.com/ylab-hi/ScanNeo2/main/environment.yml
mamba activate scanneo2
Note: The exitron module in ScanNeo2 requires apptainer (formerly singularity) which needs to be installed. If this is not provided (as usually on HPC systems), the environment_apptainer.yml can be used for that. If the exitron module is deactivated (activate: false), apptainer is not required.
In the following Scanneo2 needs to be deployed. For that, create a working directory and enter it, e.g.
mkdir -p /path/to/working/directory/
cd /path/to/working/directory/
Now the workflow needs to be deployed which can be done using
git clone recurse-submodules https://github.com/ylab-hi/scanneo2
To configure this workflow, modify config/config.yaml according to your needs, following the explanations provided in the file. It is to be noted that each parameter can also be specified over the command line. For a detailed description of the parameters, please refer to section about the configuration in the wiki. Different locations of configuration files can be specified using --configfile config.yaml.
In addition, the parameters can also be specified using the command line such as --config parameter=value. This is not recommended as this can be done on the top-level.
Given that the workflow has been properly deployed and configured, it can be executed as follows.
For running the workflow while deploying any necessary software via conda (using the Mamba package manager by default), run Snakemake with
snakemake --cores all --software-deployment-method conda apptainer
Note: The apptainer option is only required when the exitron calling is activate (see above).
Snakemake will automatically detect the main Snakefile in the workflow subfolder and execute the workflow module that has been defined by the deployment
Can be found at .tests/integration