Programming languages

The default programming language for all our project is Python version 3.7 or newer. Your code should be compliant to PEP8 and formatted using black. Object Oriented Programming (OOP) should be used whenever possible.

For specific tasks, such as preparing figures for publication or differential expression analysis, we might rely on R.

Programming environments

The default integrated development environment (IDE) is Visual Studio Code (aka vscode). All code must be developed using vscode.

Workflow systems

Project workflows must be implemented in Nextflow. You are encouraged to use Tower to monitor your experiments.

Software environments

It is highly recommended to develop your code in isolated Docker containers using vscode and install required software using conda. The workflow cookiecutter comes preconfigured to run on Docker/Singularity containers.

Readme and manifest files

Readme and manifest files MUST be written in Markdown.

Backup your project workspace

A project workspace must be backed up using duplicacy right after you finish your experiments. Duplicacy performs versioning and bit-level deduplication, in order to minimise storage space and data transfers.