nf-core / nf-core/tools

Configbuilder: testing automated infrastructure system detection

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command line tools enhancement
Dominant language
Python
Stars
322
Forks
255
Avg merge
2d 3h
Merged PRs (30d)
5

Description

Description

The infrastructure configuration side of the app has a few automated system checks in place to detect potential HPC schedulers, container software, and the presence of a module system.

Tasks
  • Test that these checks work correctly
    • HpcCustomisation._get_scheduler()
    • HpcCustomisation._get_queues()
    • HpcCustomisation._detect_module_system()
    • FinalInfraDetails._get_container_systems()
  • Run the app on different HPC systems (if possible). Currently the following should be detected:
    - [ ] PBSPro
    - [ ] SLURM
    - [ ] SGE (Sun Grid Engine)
  • Make sure that the relevant text input fields are being auto-filled when these software/systems are detected.

We'll be working on this issue at the 2026 hackathon Sydney hub

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First steps

  1. Read the whole issue, then the project's contributing guide.
  2. Comment on the issue to say you are picking it up — it saves two people doing the same work.
  3. Fork the repository and make your change on a branch.
  4. Open a pull request that references the issue number.

Research direction

Start by locating HpcCustomisation._get_scheduler(), HpcCustomisation._get_queues(), HpcCustomisation._detect_module_system(), and FinalInfraDetails._get_container_systems(), then review the existing test setup. Exercise detection for PBSPro, SLURM, SGE, container software, and module systems where possible. Done means the checks are covered and relevant text inputs are autofilled when systems are detected.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
hpc, testing-qa
Issue type
Feature
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
42/100

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