> 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.md).

# Submit a pipeline

Configure your WDL workflow, then run it with miniwdl-fovus run.

`miniwdl-fovus` is a miniwdl-fovus package, not a separate runner. You still invoke `miniwdl-fovus run` — it just executes each task as a Fovus job instead of a local Docker container.

```
WDL workflow (miniwdl run, cfg: fovus_job)
    -> one Fovus pipeline per run          (fovus pipeline create)
    -> one Fovus job per WDL task          (fovus job create, poll status)
    -> shared storage                       (rc / stdout / stderr / outputs)
```

Fovus shared storage is mounted at one path that exists on both the miniwdl host and every Fovus compute node (`fovus storage mount`). The miniwdl run directory lives on that mount, so `container_dir == host_dir`: there is no per-task upload or download step. A task's outputs are visible to the host the instant its Fovus job finishes; inputs produced by upstream tasks are staged into each task's directory on the same mount.

<table data-card-size="large" data-view="cards"><thead><tr><th></th><th></th><th data-hidden data-card-target data-type="content-ref"></th></tr></thead><tbody><tr><td><h4><i class="fa-code" style="color:$primary;">:code:</i> Replace miniwdl runtime directives</h4></td><td>Swap WDL <code>cpu</code>/<code>memory</code> runtime attributes for Fovus tokens so the optimizer can inject optimal vCPU and memory values at runtime.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/replace-miniwdl-directives.md">Replace miniwdl runtime directives</a></td></tr><tr><td><h4><i class="fa-gear" style="color:$primary;">:gear:</i> Prepare inputs and configure WDL</h4></td><td>Upload large shared inputs to Fovus Storage and wire Fovus Tokens into <code>inputs.json</code> and <code>runtime{}</code>.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/prepare-inputs.md">Prepare inputs and configure WDL</a></td></tr><tr><td><h4><i class="fa-floppy-disk" style="color:$primary;">:floppy-disk:</i> Enable Memguard for miniWDL</h4></td><td>Turn on memory checkpointing so interrupted tasks resume from a recent checkpoint instead of restarting.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/enable-memguard.md">Enable Memguard for miniWDL</a></td></tr><tr><td><h4><i class="fa-cloud" style="color:$primary;">:cloud:</i> Run fully hosted by Fovus</h4></td><td>Submit once via the Web UI or CLI; Fovus runs <code>miniwdl-fovus run</code> and all compute on cloud infrastructure.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/fovus-hosted-manager.md">Run fully hosted by Fovus</a></td></tr><tr><td><h4><i class="fa-terminal" style="color:$primary;">:terminal:</i> Run with local miniwdl-fovus run</h4></td><td>Prerequisites, submission commands, and stop/resume behavior.</td><td><a href="/docs/pipeline/miniwdl/miniwdl-submission/local-manager.md">Run with local miniwdl-fovus run</a></td></tr></tbody></table>


---

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