(monitor)=

# Monitoring runs

After launching a workflow, GLACIER switches to the **Monitor** page. This page shows live progress, logs, and outputs for the running instance.

## Header controls

The bar at the top of the Monitor page provides run-control buttons:

| Button | Action |
|--------|--------|
| **Cancel** | Sends SIGINT to the Nextflow process (graceful stop). The pipeline will finish its current task and shut down. |
| **Kill** | Sends SIGKILL (forceful termination). Use this if Cancel does not work. |
| **Resume** | Re-launches with Nextflow's `-resume` flag, picking up from the last completed process. |
| **Restart** | Cancels the run and returns to the Parameters page so you can edit settings before launching again. |
| **Open Results Folder** | Opens the instance directory in your file manager. |

## Progress tab

The Progress tab shows a tree view of the pipeline's processes, organised by group (e.g. `AMPLICON_NF:BUILD_REFERENCE`).

Each process node displays:

- **Status icon** — pending (grey), submitted (blue), completed (green), or error (red).
- **Name** — the process name from the Nextflow workflow.
- **Progress bar** — for processes with multiple tasks, shows completion percentage.

Click the **⋮** menu on a process node to view its log files:

| Option | Shows |
|--------|-------|
| `.command.out` | Standard output of the process task. |
| `.command.err` | Standard error of the process task. |
| `.command.log` | Combined log from the process task. |
| `.command.run` | The wrapper script Nextflow generated. |
| `.command.sh` | The shell command that was executed. |
| `.command.trace` | Resource usage trace for the task. |
| `.command.begin` | Timestamp when the task started. |
| **Open folder** | Opens the task's work directory in your file manager. |

The tree auto-refreshes every 5 seconds.

## Reports tab

The Reports tab lists HTML report files found in the instance output directory (excluding files inside the `work/` subdirectory). Select a report to preview it in an embedded viewer.

Typical reports generated by ARTIC workflows include:

- `articMinIONReport.html` — sequencing run summary.
- `articNcovNanoporeReport.html` — SARS-CoV-2 analysis report.

## Logs tab

Three sub-tabs provide live-updating logs:

| Tab | Source | Refresh rate |
|-----|--------|--------------|
| **stdout** | `stdout.log` (Nextflow's standard output). | 1 second |
| **stderr** | `stderr.log` (Nextflow's standard error). | 1 second |
| **nextflow.log** | Nextflow's internal log file. | 1 second |

Log content is rendered with ANSI colour support for readability.