> 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/nextflow/pipeline-submission/fovus-hosted-manager.md).
# Run fully hosted by Fovus
Submit a Nextflow pipeline to run entirely on Fovus infrastructure with no local Nextflow process after submission.
Submit a pipeline once and Fovus provisions a cloud **headnode** to run the Nextflow manager plus compute nodes for each process. Your local machine can disconnect after submission — the pipeline keeps running until it completes, fails, or you stop it.
## What Fovus-hosted means
* Fovus runs the Nextflow **headnode** and all compute jobs on cloud infrastructure.
* No local Nextflow install or `/fovus-storage` mount is required to submit.
* The pipeline continues if you close your laptop or lose connectivity.
* When the pipeline **completes, fails, or is stopped**, the headnode shuts down. Use **Stop** and **Resume** (UI or CLI) to release resources or start a new headnode — see [Stop and resume a pipeline](/docs/pipeline/monitor-manage/stop-resume-pipeline.md).
## Before you begin
1. Access to a Fovus workspace.
2. A pipeline folder with your Nextflow script and `nextflow.config` (see [Prepare inputs and configure Nextflow](/docs/pipeline/nextflow/pipeline-submission/prepare-inputs.md)).
3. [Fovus CLI](https://help.fovus.co/cli/) installed and authenticated (CLI path only).
## Submit a pipeline
{% tabs %}
{% tab title="CLI" %}
Use [`fovus pipeline create`](https://help.fovus.co/cli/commands/pipeline/create.html) to submit from a pipeline folder. Basic example:
```bash
fovus pipeline create ./my-pipeline \
--name "My RNA-seq Pipeline" \
--run-command "nextflow run main.nf"
```
With optional flags:
```bash
fovus pipeline create ./my-pipeline \
--name "RNA-seq Run 1" \
--run-command "nextflow run main.nf -profile docker" \
--setup-command "git clone https://github.com/fovus/rnaseq" \
--project-name "oncology-q1" \
--auto-delete-days 30 \
--workflow-host remote
```
`--auto-delete-days` schedules the pipeline for permanent deletion once it finishes — see [Auto-delete a pipeline](/docs/pipeline/monitor-manage/auto-delete-pipeline.md).
{% hint style="info" %}
After a successful create, Fovus writes the pipeline ID to `./my-pipeline/.fovus/pipeline_data.json`. Later `fovus pipeline resume` and `fovus pipeline stop` commands for that folder read this file automatically. Use `--override` on a second create to replace the stored ID.
{% endhint %}
You can also pass a JSON config file with `-c`:
```bash
fovus pipeline create ./my-pipeline -c pipeline-config.json
```
Example `pipeline-config.json` (field names match the [CLI reference](https://help.fovus.co/cli/commands/pipeline/create.html)):
```json
{
"name": "My Pipeline",
"projectName": "oncology-q1",
"autoDeleteDays": 30,
"workflowHost": "remote",
"configuration": {
"workflowManager": "NEXTFLOW",
"setupCommand": "git clone https://github.com/fovus/rnaseq",
"runCommand": "nextflow run main.nf"
}
}
```
For all flags, JSON options, and examples, see [fovus pipeline create](https://help.fovus.co/cli/commands/pipeline/create.html).
{% endtab %}
{% tab title="Web UI" %}
The create wizard has three steps. **Pipeline name**, **Project**, and **Auto delete** stay in the header across all steps. **Import** and **Export** are in the header too — see [Export and import configuration](#export-and-import-configuration).
**Open the wizard**
Click **Pipelines** in the top navigation, then **Create pipeline**.
**Step 1 — Workflow Manager**
Enter a **Pipeline name**, click **Nextflow**, then **Next**.
**Step 2 — Configuration**
| Field | Required | Notes |
| -------------------- | -------- | --------------------------------------------------------------------------------------- |
| **Setup command** | No | Runs on the headnode before Nextflow (e.g. `git clone https://github.com/fovus/rnaseq`) |
| **Nextflow command** | Yes | Command Fovus runs (e.g. `nextflow run main.nf`) |
{% hint style="warning" %}
**Nextflow command** is required — **Next** is disabled until it is filled in.
{% endhint %}
Click **Next**.
**Step 3 — Inputs**
Use **Import pipeline folder** or drag files into the table. Wait for uploads to finish, then click **Create pipeline**.
{% hint style="info" %}
Step 3 is optional when a **Setup command** fetches inputs at runtime — you can leave the table empty and click **Create pipeline**.
{% endhint %}
{% hint style="info" %}
The Web UI always creates a Fovus-hosted pipeline. For a local Nextflow manager, use the CLI with `--workflow-host local` or run `nextflow run` directly — see [Local Nextflow manager](/docs/pipeline/nextflow/pipeline-submission/local-hosted-manager.md).
{% endhint %}
{% endtab %}
{% endtabs %}
## Export and import configuration
Save or reuse a pipeline setup as JSON:
* **Export** — from the pipeline detail page header, or from the create wizard after **Pipeline name**, workflow manager, and **Nextflow command** are filled in. Downloads a JSON file you can edit or share.
* **Import** — click **Import** in the wizard to load `name`, workflow manager, setup command, and run command from a JSON file. You can also pass that file to the CLI with `fovus pipeline create -c pipeline-config.json`.
There is no `fovus pipeline get` command. To reuse a configuration from the terminal, export JSON from the Web UI first, then submit with [`fovus pipeline create -c`](https://help.fovus.co/cli/commands/pipeline/create.html).
## After submission
The pipeline appears in the **Pipelines** list with status **Created**, then **Running** once the headnode starts. Open the pipeline to confirm the **Nextflow command** and **Workflow host** (Remote) on the **Pipeline** tab.
See [Monitor your pipeline](/docs/pipeline/monitor-manage/pipeline-monitoring.md) to track progress and outputs.
## What's next?
---
# Agent Instructions
This documentation is published with GitBook. GitBook is the documentation platform designed so that both humans and AI agents can read, navigate, and reason over technical content effectively. Learn more at gitbook.com.
## Querying This Documentation
If you need additional information that is not directly available in this page, you can query the documentation dynamically by asking a question.
Perform an HTTP GET request on the current page URL with the `ask` query parameter, and the optional `goal` query parameter:
```
GET https://help.fovus.co/docs/pipeline/nextflow/pipeline-submission/fovus-hosted-manager.md?ask=&goal=
```
`ask` is the immediate question: it should be specific, self-contained, and written in natural language.
`goal` is optional and describes the broader end goal you are ultimately trying to accomplish on behalf of the user. GitBook uses it to tailor the answer towards what is most useful for that goal.
The response will contain a direct answer to the question and relevant excerpts and sources from the documentation.
Use this mechanism when the answer is not explicitly present in the current page, you need clarification or additional context, or you want to retrieve related documentation sections.