README.md

Rhea pipeline

Snakemake workflow for general purpose RNA-Seq library annotation developed by the Zavolan lab.

Reads are processed, aligned, quantified and analyzed with state-of-the-art tools to give meaningful initial insights into various aspects of an RNA-Seq library while cutting down on hands-on time for bioinformaticians.

Below is a schematic representation of the individual workflow steps ("pe" refers to "paired-end"):

For a more detailed description of each step, please refer to the pipeline documentation.

Requirements

Currently the workflow is only available for Linux distributions. It was tested on the following distributions:

• CentOS 7.5
• Debian 10
• Ubuntu 16.04, 18.04

Installation

Cloning the repository

Traverse to the desired path on your file system, then clone the repository and move into it with:

git clone ssh://git@git.scicore.unibas.ch:2222/zavolan_group/pipelines/rhea.git
cd rhea

Installing Conda

Workflow dependencies can be conveniently installed with the Conda package manager. We recommend that you install Miniconda for your system (Linux). Be sure to select Python 3 option. The workflow was built and tested with miniconda 4.7.12. Other versions are not guaranteed to work as expected.

Installing dependencies

For improved reproducibility and reusability of the workflow, each individual step of the workflow runs in its own Singularity container. As a consequence, running this workflow has very few individual dependencies. It does, however, require Singularity to be installed on the system running the workflow. As the functional installation of Singularity requires root privileges, and Conda currently only provides Singularity for Linux architectures, the installation instructions are slightly different depending on your system/setup:

For most users

If you do not have root privileges on the machine you want to run the workflow on or if you do not have a Linux machine, please install Singularity separately and in privileged mode, depending on your system. You may have to ask an authorized person (e.g., a systems administrator) to do that. This will almost certainly be required if you want to run the workflow on a high-performance computing (HPC) cluster. We have successfully tested the workflow with the following Singularity versions:

• v2.4.5
• v2.6.2
• v3.5.2

After installing Singularity, install the remaining dependencies with:

conda env create -f install/environment.yml

As root user on Linux

If you have a Linux machine, as well as root privileges, (e.g., if you plan to run the workflow on your own computer), you can execute the following command to include Singularity in the Conda environment:

conda env create -f install/environment.root.yml

Activate environment

Activate the Conda environment with:

conda activate rhea

Installing non-essential dependencies

Most tests have additional dependencies. If you are planning to run tests, you will need to install these by executing the following command in your active Conda environment: