Monitoring runs

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.

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