All participants should undertake some prepatation to ensure a smooth experience during the workshop.

All participants will be expected to:

  • have access to a computer with internet access
  • have access to a Linux terminal
  • understand how to program in bash, shell, python, R, or similar
  • be able to use Zoom (for active participants)
  • read over all the specific requirements for each training session

Monday sessions

Common Workflow Language (CWL) (09:30-12:00) drawing drawing drawing drawing

Preparation advice: setup instructions can be found here: https://www.commonwl.org/user_guide/setup.html

Course material: https://www.dropbox.com/sh/zvgsn0qj7lclgmp/AAALVMqrnGJb2CiC27e1TNQaa/20211129?dl=0&subfolder_nav_tracking=1

workflUX - the Workflow User eXperience (13:00-14:00) drawing drawing

Preparation advice: the session will make use of the de.NBI cloud so an ELIXIR account is required. Register here: https://elixir-europe.org/register or write an email to c.feuerstein@dkfz.de to request access.

Course material: https://github.com/CompEpigen/workflUX/blob/master/tutorials/Covid19_MSA_Group_Comparison.md

WESkit: GA4GH-compliant workflow execution (14:00-15:00)drawing drawing

Preparation advice: no special preparation is required for active participants via Zoom. For those watching the twitch stream, please read the setup instructions here: https://gitlab.com/one-touch-pipeline/weskit/documentation/-/blob/master/deployment/getting_started.md

Course material: coming soon! Until then, check out the getting started guide: https://gitlab.com/one-touch-pipeline/weskit/documentation/-/blob/master/deployment/getting_started.md

Tuesday sessions

Snakemake (09:30-12:00) drawing

Preparation advice: the course will use gitpod in your browser, so no installation or setups required. However, please register yourself at https://gitpod.io.

Course material: https://snakemake.readthedocs.io/en/stable/tutorial/short.html

OpenEBench (13:00-14:30) drawing drawing

Preparation advice: the hands-on exercises require having git, Docker and Nextflow installed locally.

Course material: https://github.com/inab/TCGA_benchmarking_workflow/blob/master/README.md

Wednesday sessions

Nextflow (09:30-12:00) drawing

Preparation advice: participants will undertake the tutorial in a cloud environment delivered via Gitpod. All you need is a browser and internet connection. Make sure to have a GitHub account and register for a free Gitpod account.

Course material: https://nextflow-io.github.io/elixir-workshop-21/docs/

nf-core (13:00-15:00) drawing

Preparation advice: participants should install Nextflow and Docker. Further instructions here: https://nf-co.re/usage/installation

Course material: https://nf-co.re/usage/tutorials/nf_core_tutorial