> 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/miniwdl/miniwdl-submission/fovus-hosted-manager.md).
# Run fully hosted by Fovus
Submit a miniWDL pipeline to run entirely on Fovus infrastructure with no local miniwdl-fovus process after submission.
Submit a pipeline once and Fovus provisions a cloud **headnode** to run `miniwdl-fovus run` plus compute nodes for each task. 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 `miniwdl-fovus run` and all task jobs on cloud infrastructure.
* No local miniwdl-fovus 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 WDL workflow and `inputs.json` (see [Prepare inputs and configure WDL](/docs/pipeline/miniwdl/miniwdl-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) with `--workflow-manager mini_wdl` to submit from a pipeline folder. Basic example:
```bash
fovus pipeline create ./my-pipeline \
--workflow-manager mini_wdl \
--name "My WDL Pipeline" \
--run-command "miniwdl-fovus run hello.wdl -i inputs.json"
```
{% hint style="warning" %}
`--workflow-manager mini_wdl` is required — when omitted, `fovus pipeline create` defaults to Nextflow.
{% endhint %}
With optional flags:
```bash
fovus pipeline create ./my-pipeline \
--workflow-manager mini_wdl \
--name "WDL Run 1" \
--run-command "miniwdl-fovus run hello.wdl -i inputs.json" \
--setup-command "git clone https://github.com/fovus/wdl-workflow" \
--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": "MINI_WDL",
"setupCommand": "git clone https://github.com/fovus/wdl-workflow",
"runCommand": "miniwdl-fovus run hello.wdl -i inputs.json"
}
}
```
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**, choose **miniWDL** from the workflow manager dropdown, then **Next**.
**Step 2 — Configuration**
| Field | Required | Notes |
| ------------------------- | -------- | -------------------------------------------------------------------------------------------- |
| **Setup command** | No | Runs on the headnode before miniWDL (e.g. `git clone https://github.com/fovus/wdl-workflow`) |
| **miniwdl-fovus command** | Yes | Command Fovus runs (e.g. `miniwdl-fovus run hello.wdl -i inputs.json`) |
{% hint style="warning" %}
**miniwdl-fovus 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 miniwdl-fovus process, use the CLI with `--workflow-host local` or run `miniwdl-fovus run` directly — see [Run with local miniwdl-fovus run](/docs/pipeline/miniwdl/miniwdl-submission/local-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 **miniwdl-fovus 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 **miniwdl-fovus 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?
---
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