Running from the UI
Pipelines can be run directly from the Adagio web interface without any additional setup.
Starting a run
From the home screen, click Run next to a saved pipeline. You can also run directly from the canvas by clicking Run in the toolbar.
Adagio will open the run configuration panel, which shows:
- Required inputs — files or data that must be provided before the run can start.
- Open parameters — any parameters that were left configurable when the pipeline was built.
- Output location — where results will be written.
Fill in the required values and click Submit.
Providing inputs
For each required input, you will be prompted to upload a file or select one you have previously uploaded. Adagio accepts QIIME2 artifact files (.qza) and metadata files (.tsv, .csv) depending on what the pipeline expects.
Monitoring progress
After submitting, the run view shows each pipeline step with a status indicator:
| Status | Meaning |
|---|---|
| Pending | Waiting to start |
| Running | Currently executing |
| Complete | Finished successfully |
| Failed | Encountered an error |
Click any step to see its log output. If a step fails, the log will include the error message to help diagnose the problem.
Results
When the run completes, results are available in the run view. You can download individual output files or the full output set.
Reruns and caching
If you rerun a pipeline with the same inputs but different parameters, only the steps affected by the change re-execute. Upstream steps whose inputs have not changed are replayed from cache automatically.
To force a full rerun from scratch, choose Rerun (no cache) from the run menu.
Downloading for CLI use
From the run configuration panel you can download an arguments file — a JSON file that captures the inputs and parameters you specified. This file can be passed directly to the adagio CLI to reproduce the same run outside the browser. See Running with the CLI.