> For the complete documentation index, see [llms.txt](https://help.fovus.co/docs/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.fovus.co/docs/pipeline/monitor-manage/stop-resume-pipeline.md).

# Stop and resume

Stop or resume a Fovus-hosted pipeline from the UI or CLI after the headnode stops.

{% hint style="warning" %}
**Stop**, **Resume**, and the CLI commands on this page apply to **Fovus-hosted** pipelines only.
{% endhint %}

## Stop a pipeline

Stopping releases compute resources but preserves Nextflow state under `/fovus-storage/pipelines/` so you can resume later.

{% tabs %}
{% tab title="Web UI" %}

1. Open the pipeline detail page for a **Running** Fovus-hosted pipeline.
2. Click **Stop** in the page header (enabled only when status is **Running** and workflow host is **Remote**).
3. Confirm in the **Stop pipeline?** dialog.

![](https://2108897467-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhGluyldqdG6yHzilfIdu%2Fuploads%2Fgit-blob-189bd05fa2dfbe70ce9d6e53d27db4f13b356da2%2Fstop-resume-pipeline-detail-header-stop.png?alt=media)

Status changes to **Stopped**. Running jobs terminate and cloud instances are released.
{% endtab %}

{% tab title="CLI" %}

```bash
fovus pipeline stop --pipeline-id <pipeline-id>
```

If you created the pipeline from a directory with `.fovus/pipeline_data.json`, pass the pipeline directory context used by your CLI setup, or specify `--pipeline-id` explicitly.
{% endtab %}
{% endtabs %}

## Resume a pipeline

Resume after status **Stopped** or **Failed** to launch a new headnode and continue orchestration.

{% tabs %}
{% tab title="Web UI" %}

1. Open a pipeline with status **Stopped** or **Failed**.
2. Click **Resume** in the page header (same area as **Stop** while the pipeline was running). Fovus opens the **Resume pipeline** page.
3. Update the **Setup command** or **Nextflow command**, add or change input files if needed, then click **Resume pipeline**.

![](https://2108897467-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhGluyldqdG6yHzilfIdu%2Fuploads%2Fgit-blob-7bba34d1bdf16352a31af00cea838742b75bfc5f%2Fstop-resume-pipeline-detail-header-resume.png?alt=media)

Fovus provisions a new headnode and restarts Nextflow. While a pipeline is **Running**, use the **Progress** tab to tail `fovus-std.out` live output.

![](https://2108897467-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2FhGluyldqdG6yHzilfIdu%2Fuploads%2Fgit-blob-a607e5e1e9bb71e141304e6560e8b109a92b749e%2Fstop-resume-progress-tab-live-output.png?alt=media)
{% endtab %}

{% tab title="CLI" %}
**From a pipeline directory**

Resume from the same folder you used for `fovus pipeline create`. Fovus reads the pipeline ID from `.fovus/pipeline_data.json`, re-uploads files from that folder, then restarts the headnode:

```bash
fovus pipeline resume ./my-pipeline
```

Fovus adds Nextflow `-resume` automatically — do not add `-resume` to `--run-command`.

**By pipeline ID**

When you do not have the original directory (or no stored ID in `.fovus/pipeline_data.json`), pass `--pipeline-id` and omit the directory path:

```bash
fovus pipeline resume --pipeline-id <pipeline-id>
```

**Change run or setup commands**

Optional on either form above — override what runs on the new headnode:

```bash
fovus pipeline resume ./my-pipeline \
  --run-command "nextflow run main.nf -profile docker" \
  --setup-command "git clone https://github.com/org/repo"
```

```bash
fovus pipeline resume --pipeline-id <pipeline-id> \
  --run-command "nextflow run main.nf -profile docker"
```

See [fovus pipeline resume](https://help.fovus.co/cli/commands/pipeline/resume.html) for all flags.
{% endtab %}
{% endtabs %}

## What's next?

* [**Monitor your pipeline**](/docs/pipeline/monitor-manage/pipeline-monitoring.md) — status, jobs, files, and infrastructure
* **Run fully hosted by Fovus** — submit and configure pipelines: [Nextflow](/docs/pipeline/nextflow/pipeline-submission/fovus-hosted-manager.md) or [miniWDL](/docs/pipeline/miniwdl/miniwdl-submission/fovus-hosted-manager.md)
* [**fovus pipeline stop**](https://help.fovus.co/cli/commands/pipeline/stop.html) and [**fovus pipeline resume**](https://help.fovus.co/cli/commands/pipeline/resume.html) — CLI reference


---

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