Catalogues

Catalogues#

A catalogue is a curated collection of workflow listings stored as a Git repository. Each catalogue contains a catalogue.json file that defines sections and the workflows within them.

Adding a catalogue#

  1. Click the Actions button in the Library page.

  2. Choose Add a Catalogue.

  3. Enter the repository identifier in owner/repo format (e.g. artic-network/glacier-catalogue).

    You can also use a shorthand org name (e.g. artic-network), but this only works if that organisation has a repository named glacier-catalogue. When in doubt, use the full owner/repo form.

GLACIER clones the repository to your config directory and parses catalogue.json to display the catalogue.

Browsing a catalogue#

Catalogues are displayed as cards. The ARTIC Network catalogue is styled with a teal colour scheme and contains three sections:

workshop#

Contains:

  • amplicon-nf — amplicon-based sequencing analysis (artic-network/amplicon-nf, latest version).

  • raccoon-nf — recombinant analysis pipeline (artic-network/raccoon-nf, latest version).

general#

General-purpose workflows:

  • amplicon-nf — same workflow as above, pinned to the 0.6.1 release.

MPXV#

Mpox virus analysis workflows with a distinct red colour scheme:

  • amplicon-nf — MPXV-specific amplicon analysis.

  • squirrel-nf — squirrel-related analysis (artic-network/squirrel-nf).

Installing workflows from a catalogue#

Each workflow card shows an Install button if the workflow is not yet cloned locally. Click it to clone the workflow repository.

You can also batch-install all workflows in a section or an entire catalogue using the ⋮ menu on the section or catalogue header, then selecting Install all workflows.

Organising catalogue contents#

Use the ⋮ menu on any section or workflow card:

Action

Effect

Hide section

Collapses the section from view. Use Show all workflows on the catalogue menu to restore.

Remove section

Deletes the section from the local copy of catalogue.json.

Hide repository

Hides an individual workflow card.

Remove repository

Removes the workflow from its section in catalogue.json.

These modifications only affect your local copy of the catalogue. They are useful for decluttering.

Checking for updates#

For workflows tracked with "version": "latest", GLACIER can check whether a newer commit is available on the default branch.

  • Use Check for updates on a single workflow card, or on a section/catalogue to check all workflows at once.

  • If an update is found, GLACIER will offer to pull the latest changes.

Adding user workflows#

You can add your own workflow repositories outside of any curated catalogue:

  1. Actions → Add Repository.

  2. Enter a display name, the GitHub URL, and optionally a version tag.

  3. The workflow is added to a special User collection catalogue that GLACIER creates automatically.

Removing a catalogue#

Use the ⋮ menu on the catalogue card and select Remove catalogue. This deletes the cloned catalogue repository from disk — it does not affect any installed workflows.

Default parameters#

Each workflow entry in a catalogue can include a parameters object that provides default values for the Parameters form. When you create an instance from a catalogue entry that has default parameters, those values are pre-filled automatically.

Example catalogue.json:

{
  "name": "My Catalog",
  "sections": [
    {
      "name": "Genomics",
      "workflows": [
        {
          "name": "amplicon-nf",
          "repo": "artic-network/amplicon-nf",
          "version": "main",
          "parameters": {
            "outdir": "./results",
            "primer_set": "SARS-CoV-2/V1200"
          }
        }
      ]
    }
  ]
}

The precedence for parameter values (highest to lowest) is:

  1. User settings — Auto-resolved values like outdir and store_dir from GLACIER settings

  2. Catalogue defaults — The parameters object in the catalogue entry

  3. Schema defaults — Defaults defined in the workflow’s nextflow_schema.json

This means catalogue defaults are a convenient starting point, and they can be overridden by GLACIER’s auto-resolution settings or by direct changes in the Parameters form.

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