Running V-Pipe on ELIXIR On Cloud (main workflow)

[gordonkoehn]

Why

V-Pipe runs the Swiss national program to monitor viral variants (Sars-CoV-2, RSV and Influenza-A/B).
It has so far been deployed in cluster settings and we'll bring it to the cloud for more dynamic interactions.

What

• Fetch user-defined public ENA raw sequencing data
• Run the the V-Pipe workflow on a cloud instance
• Store intermediate Outputs in S3 Buckets
• Lightweight Frontent of Mutation Variant Calling (to be expanded)

How

• Deployment: Docker and / or WES execution, within a kubernetics setting
• Within the new in loculus platform for sequence storage and sharing
• Advanced Snakemake Workflow (V-Pipe / additional wrappers)
• Frontend: e.g. Streamlit or similar

Task List:

• TBD