Workflows

Workflows#

A workflow is a pipeline stored in a Git repository. GLACIER currently supports Nextflow workflows, detected by the presence of a nextflow_schema.json file.

Installing a workflow#

From the Library page, click Install on any workflow card. GLACIER clones the repository to your workflows directory at <configPath>/workflows/<owner>/<repo>@<version>.

The button label changes from Install to Launch once the clone completes.

Configuring parameters#

Click an installed workflow card to open the Parameters page. This page has three tabs:

Info#

Renders the workflow’s README.md so you can review documentation before running.

License#

Shows the LICENSE file from the workflow repository.

Params#

The main configuration view. GLACIER reads the workflow’s nextflow_schema.json and renders a JSON Forms form. You can:

  • Edit parameter values directly in the form.

  • Load parameters from a .json file on disk.

  • Save parameters to a .json file for reuse.

Execution profiles#

The Profiles dropdown lists profiles extracted from nextflow.config. These map to Nextflow’s -profile flag. The standard profile is selected by default.

If a test profile exists, a Test launch button appears alongside Launch. Use this to run the workflow with the test profile combined with your other selections.

Resource requirements#

Workflow repositories can include a glacier.json file at the root to specify minimum CPU and memory requirements:

{
  "resources": {
    "minimum": {
      "cpus": 4,
      "memory": 8
    }
  }
}

When you open the Parameters page for a workflow that has a glacier.json, GLACIER checks your system against the minimums. A warning banner appears if your effective resources (accounting for GLACIER resource limits, WSL config on Windows, and system hardware) are below the workflow’s recommendations. You can still launch the workflow despite the warning.

Launching a workflow#

When you click Launch, GLACIER:

  1. Validates parameters against the JSON Schema (unless disabled in Settings).

  2. Creates a workflow instance — a named run directory containing the parameters file, logs, and work directory.

  3. Spawns the Nextflow process using the bundled JRE and nextflow.jar.

  4. Navigates to the Monitor page so you can follow progress in real time.

Launch options#

Option

Behaviour

Launch

Starts the pipeline with selected profiles and parameters.

Test launch

Available when a test profile exists. Runs with test plus any other selected profiles.

Resume and restart#

  • Resume (from Monitor page) — re-launches with Nextflow’s -resume flag, continuing from the last checkpoint.

  • Restart (from Monitor page) — cancels the running instance and opens the Parameters page so you can edit settings before re-launching.

What happens after launch#

Nextflow is invoked with the following flags:

java -jar nextflow.jar run <repo> \
  -work-dir <instance_path>/work \
  -profile <profiles> \
  -params-file <instance_path>/params.json \
  -name <instance_name>

Standard output and error are captured to stdout.log and stderr.log in the instance directory. Nextflow’s own log goes to nextflow.log.

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