DevOps Containers

This repository hosts a collection of reusable container images designed to support various stages of data processing pipelines, with a focus on single-cell genomics analysis workflows, and more specifically for scRNA-seq and scATAC-seq.

These containers are built to be modular, consistent, and reproducible, ensuring reliable execution across a wide range of environments, including local development, cloud platforms, and CI/CD systems.

Although primarily used within automated pipelines — such as

• sc-rna-seq-snap
• sc-rna-seq-snap-10x-Flex
• sc-epigenie

each container is self-contained and portable, making it easy to use them independently in other projects or custom workflows. This flexibility makes the containers valuable tools for both bioinformatics and DevOps tasks where reproducibility and scalability are key.

🚀 Key Features

• Reusable: Designed to be used across multiple pipelines and projects
• Versioned & Maintainable: Each container is built with version control in mind
• Isolated: Minimal dependencies ensure consistent and portable environments
• Well-Documented: Each container folder includes its own README.md with build/run instructions

Table of Contents

1. Accessing the Container
2. Using the Container for a scRNA-seq project
3. Using the Container for a scATAC-seq project

Accessing the Container

Users can clone the devops-containers repository to their local machine to access and run the container of their preference.

git clone https://github.com/stjude-dnb-binfcore/devops-containers.git

or they can fork the repository.

Using the Container for a scRNA-seq project

Users can add their own code to the module of interest at ./devops-containers/analyses/sc-rna-seq/<my_project>. Afterward, follow the instructions in the README.md to pull and access the container.

Using the Container for a scATAC-seq project

Users can add their own code to the module of interest at ./devops-containers/analyses/sc-atac-seq/<my_project>. Afterward, follow the instructions in the README.md to pull and access the container.

Below is the main directory structure listing the analyses and data files used in this repository

├── analyses
|  ├── sc-atac-seq
|  |   ├── myproject
|  |   └── run-container
|  └── sc-rna-seq
|      ├── myproject
|      └── run-container
├── figures
├── LICENSE
├── README.md
└── SECURITY.md

Authors

Antonia Chroni, PhD (@AntoniaChroni)

Contact

Contributions, issues, and feature requests are welcome! Please feel free to check issues.

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These tools and pipelines have been developed by the Bioinformatic core team at the St. Jude Children's Research Hospital. These are open access materials distributed under the terms of the BSD 2-Clause License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.