Introduction

ENEO is a Snakemake workflow developed for the identification of cancer neoantigens using solely the tumor RNAseq, without requiring matched controls or additional sequencing experiments. You could read more from the publication here.

Quick Start

To execute the pipeline, it's required to have both snakemake and singularity or apptainer installed. The easiest way to install both of them is using a dedicated conda environment. To create a new environment, use the following commands:

conda create -c conda-forge -c bioconda -c nodefaults -n snakemake snakemake apptainer

To start, clone the repo using

git clone https://github.com/ctglab/ENEO.git

The next step is to setup resources, as reported in the dedicated section.

Then update the configuration file in config/config.yaml following the instructions in the dedicated section.

The next step is to setup patients and their relative sequencing files, defined in the files units.csv and patients.csv. The pipeline is designed to be executed both from paired end FASTQ files. Edit then the units.csv file to specify the absolute path for sequencing files of each patient, accordingly:

• if you're executing the pipeline in full mode, you had to provide paths to the paired end fastq files, as detailed.

  patient,fq1,fq2
  Pat_01,/path/to/Pat_01_1.fastq.gz,/path/to/Pat_01_2.fastq.gz
  Pat_02,/path/to/Pat_02_1.fastq.gz,/path/to/Pat_02_2.fastq.gz
  

Edit also the patients.csv file to add the list of patients to be processed. All the listed patients must match the patients in the units.csv file.

```
patient
Pat_01
Pat_02
```

Executing the pipeline

If you're running the pipeline using an HPC cluster, we provided detailed execution profiles for SLURM schedulers under the workflow/profile directory and the relative instruction in the dedicated section.

Alternatively, you can run the pipeline locally, using the following command:

snakemake \
--use-singularity \
--cores 8 \
--singularity-args "-B /path/to/ENEO -B /path/to/ENEO_output -B /path/to/ENEO_temp -B /path/to/eneo_resources --env TMPDIR=/path/to/ENEO_temp"

Reporting issue

If you encounter any error in the pipeline setup/execution, or you have any question regarding its usage, fill an issue on github