Overview
Reproducible research is an important part of good scientific practice. Establishing robust computational analysis workflow facilitates reproducible research. There has been a strong emphasis on establishing graphic workflow management systems, such as Galaxy and Knime. However, the landscape and complexity of Linux command line tools for workflow management is vast and complicated. We aim to take advantage of European/International leaders in the field to present current scientific workflow paradigms and a lead workshops to implement a basic workflow. Topics covered include workflows and containerization.
Learning objectives
Docker
- Understand what containerisation is, and why you might use it in bioinformatics
- Be familiar with Docker; basic concepts and structure
- Find and run containers built by other people
- Build your own application into a container (containerisation)
- Distribute your container online
CWL
- Understand syntax and structure for CWL
- Understand how to write CWL tool definitions for command line tools
- Read and write CWL files written in YAML
- How to run CWL workflows locally and on EG-CI
- Join CWL tools into a workflow
- Use Docker with CWL to provide software dependencies and ensure reproducibility
Audience and requirements
This introductory tutorial is aimed towards bioinformaticians (graduate students and researchers), who are interested in becoming familiar to Docker based workflows in CWL, as is currently supported by the ΕLIXIR-Greece Compute Infrastructure (EG-CI).
Prerequisites
- Experience in Shell; this includes basic commands (such as
ls,cp,mv,nano/vim) and operations such as (apt, installing tools etc).
Maximum participants: 25
Schedule
Day 1
| Time | Details |
|---|---|
| 10:00 - 10:30 | Tutorial introduction. - Get to know each other. - Setup Link to material |
| Part I: Containers Background | |
| 10:30 - 11:30 | Introduction to Containerization. - Concepts and Theory Link to material |
| 11:45 - 13:00 | Run a container. - Examples of how to run an existing Docker container Link to material |
| Part II: Building a Container | |
| 14:00 - 15:30 | Building a container image. - How to build a container Link to material |
| 15:45 - 17:00 | Distribute online - What are the available options (DockerHub, GitHub) Link to material |
| 17:00 | Closing, discussion and feedback |
Day 2
| Time | Details |
|---|---|
| 09:00 - 09:30 | Welcome back and Q&A. - Recap of Day 1 - Setting up for Day 2 Link to material |
| Part I: Basics of Workflow Languages | |
| 09:30 - 10:45 | Intro to workflows. - Syntax and structure of CWL Link to material |
| 11:00 - 12:30 | Writing a CWL in YAML. - Examples of tool definitions in CWL Link to material |
| Part II: Hands-on | |
| 13:30 - 14:45 | Combining tools in a workflow. - Building a complete workflow in CWL Link to material |
| 15:00 - 16:30 | Deploying a tool on EG-CI - Using the ELIXIR-GR e-infrastructure? Link to material |
| 16:30 - 17:00 | Closing, discussion and Q&A |
Registration
Dates of the workshop: 30-31/03/2020 (Postponed due to COVID-19)
Please register to the workshop using this form.
Deadline: Mon 16/03/2020 (tba)
Notifications: Wed 18/03/2020 (tba)
Venue
National Infrastructures for Research and Technology (GRNET)
Kifisias Avenue 7
115 23, Athens, GR
30-31 March, 2020
For more information, check the GRNET contact page here
Other examples
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Sources / References
The material in the workshop has been based on the following resources:
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Relevant literature includes:
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License
This material is made available under the Creative Commons Attribution 4.0 International license. Please see LICENSE for more details.
Acknowledgements
This work has been produced with the support of the RDA Europe Ambassador programme. It has received funding from the European Union’s Horizon 2020 (H2020) research and innovation programme via the RDA EU 4.0 project (ref. GA no. 777388).
Citation
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