Workshop: Interoperable Workflows Using Workflow Management Systems and Singularity Containers

Wednesday, October 4, 11 am – 5 pm Eastern time

Virtual workshop


Sponsored by the National Institute of Health’s Common Fund Data Ecosystem, and in partnership with the HuBMAP Consortium and the Brain Image Library, PSC is proud to present a workshop on using Common Workflow Language (CWL) to create interoperable workflows.

This workshop will be presented virtually.

Applications will be accepted through September 28.


Logo for the Common Fund Data Ecosystem

Part 1: Elevating Scientific Computing with Singularity Containers

11 am – 12 pm

During this session, you can expect the following

  • Overview of Singularity Containers: We’ll start with a brief overview of Singularity containers, discussing their purpose, advantages, and use cases in scientific computing.
  • Singularity Container Sharing on Discover the container sharing capabilities offered by, a powerful platform for sharing, discovering, and managing Singularity containers. We will explore how to find and use existing containers, as well as how to contribute your own containers to the community. You will learn best practices for container sharing and collaboration through the platform.
  • Container Creation and Building: Learn the step-by-step process of creating Singularity containers from scratch on Bridges-2. We’ll cover different approaches, including starting from a base image or using existing containers as a foundation. We’ll also explore how to customize and optimize containers for your specific requirements.


Break: 12 pm – 1 pm


Part 2: Streamlining Reproducible Data Analysis using Workflow Management Systems and Singularity Containers

First session: 1 pm – 2:45 pm

  • Introduction to Workflow Management Systems (WMS): A practical understanding of WMS benefits, automation, and implementation.
  • Dive into Nextflow: Through hands-on exploration and interactive sessions, attendees will discover how Nextflow simplifies the orchestration of complex data analysis pipelines.
  • Dive into Snakemake: Through practical exercises and interactive discussions, attendees will learn about Snakemake’s potential in simplifying the creation and execution of data analysis pipelines.
  • Hands-on Activity: Advanced Workflow & Debugging: Participants will optimize workflow performance and confidently handle complex scenarios, gaining valuable skills to overcome challenges in their projects.
  • Q&A

Break: 2:45 pm – 3:00 pm


Second session: 3:00 pm – 5:00 pm

  • Introduction to Common Workflow Language (CWL): Through interactive exercises and real-world examples, participants will learn how CWL standardizes workflow descriptions, making them portable and reproducible across different platforms.
  • Singularity Containers for Reproducibility: Through hands-on activities and demonstrations, participants will understand how Singularity containers encapsulate dependencies and environments, enabling seamless and consistent execution across various systems.
  • Integrating CWL with Singularity Containers: Through interactive exercises and practical examples, participants will learn how to create CWL workflows that seamlessly integrate with Singularity containers, ensuring consistent execution across diverse computing environments.
  • Hands-on Activity: Examples using HuBMAP data: Through hands-on exercises and demonstrations, attendees will gain valuable insights into data analysis, visualization, and interpretation using public HuBMAP datasets.
  • Best Practices for Workflow Optimization: Through interactive sessions and practical exercises, attendees will learn proven strategies to identify bottlenecks, streamline processes, and optimize resource utilization.
  • Hands-on Activity: Advanced Workflow & Debugging: Through hands-on exercises and demonstrations, attendees will gain valuable insights into data analysis, visualization, and interpretation using public Brain Image Library datasets.
  • Q&A