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 preprint here.

Quick Start

To execute the pipeline, it's required to have both snakemake and singularity 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 -n eneo -c bioconda snakemake=8.6.0

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 FASTQ or already aligned BAM files: this different behavior is specified using the execution_mode in the main configuration file. 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

alternatively, if you're executing the pipeline in reduced mode, you had to provide paths to the aligned bam files, as detailed.
```
patient,bam
Pat_01,/path/to/Pat_01.bam
Pat_02,/path/to/Pat_02.bam
```

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 both SLURM and SGE 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"