About Scientific Workflows

Scientific workflows are structured, automated pipelines used to process, analyze, and manage complex data sets. Tools like Snakemake and Nextflow provide frameworks for defining these workflows in a reproducible, scalable, and portable manner.  They make it easier to integrate multiple software tools and help simplify the process of scaling your analysis from running locally on your laptop to the EMBL high-performance computing cluster.

How can Scientific Workflows help your research?

• Reproducibility: Ensure consistent results by automating analysis steps and recording all parameters, software versions, and input files.
• Scalability: Efficiently process large data sets by parallelizing tasks across multiple CPUs or the HPC cluster.
• Transparency: Clarify complex analyses by making each step of the data processing pipeline explicit and easy to review.
• Efficiency: Save time and reduce errors through automation, minimizing manual intervention and repetitive tasks.
• Collaboration: Share workflows with collaborators or the broader scientific community, enhancing knowledge transfer and method dissemination.

Our Services

We offer consultation services to help EMBL researchers design, implement, and maintain scientific workflows using tools like Snakemake and Nextflow. Whether you’re starting from scratch or looking to improve existing pipelines, we provide:

• Topic introductions for those interested in using workflow management systems.
• Workflow design and development support, from simple scripts to complex, multi-step pipelines.
• Assistance with integrating workflows into the EMBL HPC cluster.
• Troubleshooting and optimization of existing workflows to improve performance and reproducibility.
• Documentation and best-practices guidance to ensure long-term maintainability.