Designing Reproducible Workflows Using Snakemake

Wednesday, 3 June 2026, 11am to 12pm

High-throughput technologies such as RNA sequencing—at both bulk and single-cell levels—generate large volumes of complex data across many samples. Ensuring that these analyses are reproducible, scalable, and portable is a major challenge in modern bioinformatics.

This hands-on training course introduces participants to the principles and practical implementation of reproducible computational workflows using Snakemake, Conda, and Docker. Participants will learn how to design structured pipelines, manage software dependencies, and containerize analyses to ensure portability across computing environments.

This session will cover:
1-Reproducibility Challenges in Bioinformatics
Common issues in managing software dependencies and scaling analyses across multiple samples.

2-Introduction to Workflow Management with Snakemake
Rules, dependencies, dry runs, and execution of a simple reproducible pipeline.

3-Environment Management with Conda
Creating isolated environments and integrating them directly into Snakemake workflows using --use-conda.

4-Containerization Concepts with Docker
Basic principles of Docker and how containers improve portability and reproducibility.

5-Combining Snakemake, Conda, and Containers
Overview of how these tools work together in modern bioinformatics pipelines.

Pre requisites:
Familiary with command line terminal

Intended audience: Anyone interested in performing bioinformatic analysis

Participants will need:
Bring your own computer
Install docker
Install Visual Code IDE

Pre-Course Preparation:
Docker, Visual Code

Duration: presentation and practical workshop.

Speaker(s): Dr Andre Aquime Goncalves (Department of Paediatrics)

Venue: Big Data Institute - Seminar room 1 - Seminar room 1 Big Data Institute Old Road Campus Oxford Oxfordshire OX3 7LF United Kingdom

Department: Big Data Institute - NDPH (Unit)

Organiser: Sumeeta Maheshwari

Host: Prof Thomas Nichols

Register here: https://forms.office.com/e/zYXRGreAKu?origin=lprLink