Onboarding

Here you can find instructions on how to run assembly projects for the VR-EBP, ERGA, and BGE projects.

To ensure consistent, reproducible, and efficient genome assembly and analysis projects, we’ve established these standard operating procedures (SOPs). By following these guidelines, we aim to optimize our workflows, streamline data management, and facilitate collaboration.

Why do we need these protocols?

  • To make data findable - (strict folder structure)
  • Ease project tracking - (git)
  • Reduce workload - (automation, code sharing)
  • Reproducibility - (workflows, notebooks, git, documentation, containers, interoperability)
  • Documentation - (reporting, summaries, issue tracking)

Getting started

A Github account is needed. A new member needs to added to the NBISweden Github organisation (ask on #technical-operations), and then to the ERGA assemblies team (Responsible: Martin P.).

New members also need to be added to the NAISS compute and storage allocations in SUPR (Responsible: Henrik / Mahesh).

Life-cyle:

flowchart LR
    onboard[onboarding] --> project
    subgraph project
        direction LR
        initialize --> launch
        launch --> monitor
        monitor --> launch
        monitor --> closing
    end

Roles:

Project roles:

  • Lead: Henrik (NBIS), Lucile (NBIS)
  • Sequencer: Ignas (NGI), Christian (NGI)
  • Assembler: Martin P. (NBIS), Mahesh (NBIS), André (NBIS), Guilherme (NBIS), Estelle (NBIS), Tomas (NBIS)
  • Annotator: Lucile (NBIS), André (NBIS), Guilherme (NBIS), Martin P. (NBIS)
  • Steward: Stephan (NBIS), Yvonne (NBIS)
  • Analyst: André (NBIS), Guilherme (NBIS)
  • Developer: Mahesh (NBIS), Martin P.(NBIS)
  • Monitor: Mahesh (NBIS)

sequenceDiagram
    actor Lead
    actor Sequencer
    actor Assembler
    actor Annotator
    actor Steward
    actor Analyst
    actor Developer
    Lead ->> Sequencer: Sequence this species
    Sequencer ->> Assembler: Sequence data delivered
    Sequencer ->> Steward: Submit read data
    Assembler ->> Annotator: Assembly finished. Annotate please.
    Annotator ->> Analyst: Annotation complete. Analyse please.
    Annotator ->> Steward: Assembly and Annotation complete. Submit it.

Who to talk to:

  • Add to Github organisation: #technical-operations
  • Add to Github team: Martin P.
  • Add to NAISS compute allocation: Henrik / Mahesh
  • Add to NAISS storage allocation: Henrik / Mahesh
  • How to use the template: Mahesh
  • Code review: Mahesh
  • Protocol review: Mahesh
  • Disk space issues: Entire team
  • Anything else: #vr-accessibility-ebp