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Running V-Pipe on ELIXIR On Cloud (main workflow) #1

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gordonkoehn opened this issue Nov 3, 2024 · 0 comments
Open
1 task

Running V-Pipe on ELIXIR On Cloud (main workflow) #1

gordonkoehn opened this issue Nov 3, 2024 · 0 comments
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@gordonkoehn @DrYak
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language: py language: snakemake topic: v-pipe type: deployment type: meta

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@gordonkoehn
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gordonkoehn commented Nov 3, 2024 •
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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
@gordonkoehn gordonkoehn self-assigned this Nov 3, 2024
@gordonkoehn gordonkoehn changed the title Running V-Pipe on ELIXIR On Cloud Running V-Pipe on ELIXIR On Cloud (main workflow) Nov 3, 2024
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language: py language: snakemake topic: v-pipe type: deployment type: meta
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BioHackathon Europe '24
Status: In progress
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@gordonkoehn @DrYak