Reproducibility is a cornerstone of good scientific practice. Thanks to funding provided by ELIXIR Training Platform Task 2, we have brought together the biggest names in bioinformatics workflow management for a 3 day practical workshop. We have presentations from the development teams of CWL, Snakemake, Nextflow, nf-core and more. If you want to learn more about the workflow management concepts that will be addressed in this workshop, check out these articles:
- Workflow systems turn raw data into scientific knowledge
- Methods Included: Standardizing Computational Reuse and Portability with the Common Workflow Language
- Sustainable data analysis with Snakemake
- Nextflow enables reproducible computational workflows
- The nf-core framework for community-curated bioinformatics pipelines
- Lessons Learned: Recommendations for Establishing Critical Periodic Scientific Benchmarking

Details

Organizers:
- Naveed Ishaque, Berlin Institute of Health at Charité University Hospital
- Sina Barysch, EMBL
- Franziska Mueller, Berlin Institute of Health at Charité University Hospital
- Daniel Wibberg, CeBiTec, Univerity of Bielefeld

Target audience: PhD/postdoc-level bioinformaticians familiar with omics analysis and scripting in python/R. You should already be familiar with some data analysis workflows and ready to take your first steps in trying out a modern workflow management tool.

Places: 30 attendees - apply soon to avoid disappointment!

Location: virtual via Zoom. The practical sessions will require use of your own laptop, HPC etc. Please note that you will be expected to set up software environments for the practical sessions before hand. Details on how to do this will be provided in due course.

Dates: Monday 29th November – Wednesday 1st December.

Contact: for more information email Naveed Ishaque, naveed.ishaque@bih-charite.de

Registration

Please register via surveymonkey

Provisional Schedule

Day 1: Monday 29th November

09:30-12:00: opening remarks
- Naveed Ishaque

09:30-12:00: CWL
- Michael R. Crusoe, Vrije Universiteit Amsterdam (VU Amsterdam), Netherlands
- Celia van Gelder, Dutch Techcentre for Life Sciences, Netherlands
- Fotis E. Psomopoulos, Centre for Research and Technology Hellas, Greece

Link to material: coming soon...

13:00-14:00: workflUX - The Workflow User eXperience
- Pavlo Lutsik, German Cancer Research Centre, Germany
- Mei-Ju Chen, German Cancer Research Centre, Germany
- Clarissa Feuerstein, German Cancer Research Centre, Germany

Link to material: coming soon...

14:00-15:00: WESkit: GA4GH-compliant workflow execution for stability and production
- Sven Twardziok, Berlin Institute of Health at Charité University Hospital, Germany

Link to material: coming soon...

Day 2: Tuesday 30th Nov

09:30-12:00: Snakemake
- Johannes Köster, University of Duisberg and Essen, Germany

Link to material: https://snakemake.readthedocs.io/en/stable/tutorial/tutorial.html

13:00-15:00: OpenEBench
- Salvador Capella-Gutierrez, Barcelona Super Computing Centre, Spain
- Laura Portell, Barcelona Super Computing Centre, Spain
- Asier Gonzalez, Barcelona Super Computing Centre, Spain

Link to material: coming soon...

Evening virtual social via gather.town - meet and discuss experiences with your peers and trainers while enjoying your favourite food delivery service!

Day 3, Wednesday 1st Dec

09:30-12:00: Nextflow
- Paolo Di Tommaso, Seqera Labs, Spain
- Evan Floden, Seqera Labs, Spain
- Luca Cozzuto, Centre for Genomics Regulation, Spain

Link to material: coming soon...

13:00-15:00: nf-core
- Gisela Gabernet, University of Tübingen, Germany
- Friederike Hanssen, University of Tübingen, Germany

Link to material: coming soon...

15:00-15:15: closing remarks

Registration

Please register via surveymonkey

Poster

For more information email Naveed Ishaque, naveed.ishaque@bih-charite.de