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The Task Library is the lab’s bookshelf of ready-to-run preprocessing templates. Each template lives in two places:
  1. Public GitHub registry – the always-current source of truth.
  2. Bundled snapshot – a copy packaged with AutoCleanEEG so everything still works when you are offline.
You do not need any programming background to use the library. Think of it like choosing a protocol from a shelf, copying it to your lab notebook, and customising a few details.
The public registry is hosted at cincibrainlab/autocleaneeg-task-registry. You never have to visit GitHub directly—the CLI fetches what it needs.

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Why scientists care

  • Stay aligned with the lab. Everyone pulls the same template before running a study.
  • Update without reinstalling software. A quick command grabs the latest version as soon as it is published.
  • Work anywhere. If the hospital blocks GitHub, the pipeline quietly falls back to the bundled snapshot.
  • Customise safely. You copy a template into your workspace before editing so the original remains untouched.

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How the pieces connect

GitHub Registry (official templates)
        |  task library update
        v
Local Cache (AutoCleanEEG config folder)
        |  used when offline or behind a firewall
        v
Packaged Snapshot (ships with the app)
        |  task library install
        v
Workspace /tasks (your editable copies)
In practice:
  1. task library update refreshes the index and records the version you now have.
  2. task library list reads your cache and shows status badges for every template.
  3. task library install <name> copies the template into your workspace so you can edit it like any other task.

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Everyday commands

# Check for new templates
autocleaneeg-pipeline task library update

# Review what is available and where each template came from
autocleaneeg-pipeline task library list --show-paths

# Copy a template into your workspace for editing
autocleaneeg-pipeline task library install RestingEyesOpen
Have your own tweaks already? Use --force to overwrite your copy, or install with a new name (for example RestingEyesOpen_v2).

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Understanding the status badges

  • up to date – your workspace copy matches the latest library version.
  • customized – you have edited the file; reinstall to compare with the original.
  • install to use – the template is available but has not been copied into your workspace yet.
  • status unknown – the CLI has not seen this template before (for example, you have never run task library update).
Whenever the CLI cannot reach GitHub it notes the error once and shows “Working offline” with the time of the last successful check. You never have to guess whether your cache is stale.

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Real-world examples

  • Resting-state study refresh. A new quality-control step is published for resting EEG. Analysts run task library update on Monday, reinstall the template, and process the week’s participants with the improved settings.
  • Multi-site collaboration. Two sites agree to use the same ASSR pipeline. Each site installs ASSR_40Hz directly from the library so their analyses match from day one.
  • Clinic check-in. A technician on a secure network installs RestingEyesQuickCheck to perform a fast quality read before starting a session. The command uses the bundled snapshot because the network blocks GitHub.

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Frequently asked questions

Do I need a GitHub account? No. The registry is public and the CLI fetches files without credentials. Will I lose my custom edits when the library updates? No. Your workspace copy is yours. Reinstalling simply places a fresh copy beside it so you can compare. Can we publish our own templates? That is on the roadmap. For now, the registry contains lab-maintained templates only.

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Keep going

  • Follow the hands-on steps in the Task Library Walkthrough.
  • Learn how to edit and organise templates locally in Task Management.
  • Curious about the engineering details? See docs/task_registry_plan.md in the pipeline repository.
Ready to start? Run: 
autocleaneeg-pipeline task library update &&   autocleaneeg-pipeline task library list --show-paths
This primes your cache so the next installation is instant.