Containers & workflows lesson hackathon

This repository contains all practical information regarding the containers & workflow pipelines training materials hackathon. A website was generated containing the created materials in an overviewable way and is available here.

Background information

The ELIXIR Training Platform ran a survey in 2019 to identify potential gaps in training courses and materials with containers and workflow pipelines considered to be one of the major identified gaps. The aim of the hackathon is to develop training materials and relevant use-cases, freely available and useful for 1) organizing courses on the topic and 2) self-learning. A plethora of choices exist as to which technologies that can be used regarding containers and workflow pipelines, however with recent increase in the popularity of Docker and Singularity containers and Nextflow pipelines, these are being put forward as technologies.

Overview hackathon program & documents:

Hackathon found place on two different day, the master repository is available at this link:

• First day: focused on drafting a framework for practical training materials, including defining learner's profiles, learning objectives and outcomes.
  • Date: 10 February 2021
  • Contribution document
• Second day: purpose of finalizing the materials and designing exercises for hands-on training.
  • Date: 6 April 2021
  • Draft program
  • Contribution documents were online edited at hackmd.io, the final documents were pushed as Markdown files into the GitHub repository.
    • outline containers training materials & exercises
    • outline workflow pipelines training materials & exercises

Materials authored during the hackathon will be publicly available through GitHub, under a CC-BY license, to be reused both within and outside ELIXIR.

For any questions and/or clarifications, please reach out to the main organizers of the hackathon

• Alexander Botzki (VIB Bioinformatics Core, ELIXIR Belgium) - [email protected] (temporarily alternative: [email protected])
• Tuur Muyldermans (VIB Bioinformatics Core, ELIXIR Belgium) - [email protected] (temporarily alternative: [email protected])

Hackathon leads

In alphabetical order:

• Alexandre Francisco (Instituto Superior Técnico Lisboa, PT)
• Alexandros Kanterakis (Institute of Computer Science, FORTH, GR)
• Alexander Botzki (VIB Bioinformatics Core, ELIXIR BE, BE)
• Geert van Geest (SIB, CH)
• John Sundh (SciLifeLab, SE)
• Jose Espinosa-Carrasco (Centre for Genomic Regulation Barcelona, ES)
• Julia Ponomarenko (Centre for Genomic Regulation Barcelona, ES)
• Luca Cozzuto (Centre for Genomic Regulation Barcelona, ES)
• Mateusz Kuzak (eScience Center, NL)
• Maxime Garcia (Nf-core, SE)
• Pedro Fernandes (The Gulbenkian Training Programme in Bioinformatics, PT)
• Renuka Kudva (Nf-core, SE)
• Sarah Bonnin (Centre for Genomic Regulation Barcelona, ES)
• Toni Harmoso Pulido (Centre for Genomic Regulation Barcelona, ES)
• Tuur Muyldermans (VIB Bioinformatics Core, ELIXIR BE, BE)