> 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/pipeline-overview.md). # Overview Understand what a Fovus Pipeline is, how it differs from a Job, and how to choose a workflow manager. Running a multi-step analysis often means managing dependencies between processes, shuffling intermediate files, and tracking which steps finished and which failed. A Fovus Pipeline automates that — you write the workflow in a supported workflow manager (**Nextflow** or **miniWDL**), and Fovus handles compute provisioning, data movement, and cost optimization for every step. ## Pipeline vs Job | | **Pipeline** | [**Job**](/docs/job/overview.md) | | ------------------- | --------------------------------------------------------------------------------------------------------------- | --------------------------------------------------- | | **Unit of work** | A full multi-step workflow (many interdependent processes) | A single compute task or a parallel parameter sweep | | **Orchestration** | The workflow manager (Nextflow or miniWDL) manages process/task dependencies; Fovus executes each step as a Job | Fovus manages task parallelism directly | | **Use case** | Bioinformatics workflows, data processing pipelines with branching logic | Simulation runs, parameter sweeps, batch rendering | | **Typical trigger** | `nextflow run` / `miniwdl-fovus run`, or Fovus Web UI / CLI pipeline creation | Fovus Web UI or CLI job submission | {% hint style="info" %} If your work is a single compute task or an embarrassingly parallel parameter sweep, use a Job. If your work is a multi-step workflow with process dependencies, use a Pipeline. {% endhint %} ## Choose a workflow manager | | **Nextflow** | **miniWDL** | | ------------------------------------ | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | | **Workflow language** | Nextflow DSL | WDL | | **Execution modes** | [Fovus-hosted](/docs/pipeline/nextflow/pipeline-submission/fovus-hosted-manager.md) (cloud headnode) or [local Nextflow manager](/docs/pipeline/nextflow/pipeline-submission/local-hosted-manager.md) | [Fovus-hosted](/docs/pipeline/miniwdl/miniwdl-submission/fovus-hosted-manager.md) (cloud headnode) or [local miniwdl-fovus run](/docs/pipeline/miniwdl/miniwdl-submission/local-manager.md) | | **Pipeline survives local shutdown** | Yes, in Fovus-hosted mode | Yes, in Fovus-hosted mode | | **Get started** | [Nextflow quickstart](/docs/pipeline/nextflow/nextflow-quickstart.md) | [miniWDL quickstart](/docs/pipeline/miniwdl/miniwdl-quickstart.md) | ## Pipeline statuses | Status | Meaning | | ------------------ | ----------------------------------------------------- | | **CREATED** | Pipeline created but not yet running | | **RUNNING** | Pipeline is actively executing | | **COMPLETED** | Pipeline finished successfully | | **FAILED** | Pipeline ended with an error | | **STOPPED** | Pipeline was stopped before completion (Fovus-hosted) | | **DELETED** | Pipeline has been removed | | **DELETE\_FAILED** | A deletion attempt failed | ## Outputs in Fovus Storage All intermediate and output files from a pipeline run are stored in [Fovus Storage](/docs/storage/storage-overview.md), under the run/work directory that the workflow manager is configured to use. For Nextflow, that directory follows a fixed structure: ``` /fovus-storage/pipelines/{pipelineId}/ ``` Published output directories (configured via Nextflow's `publishDir` directive) appear under the pipeline folder in Storage — see [Prepare inputs and configure Nextflow](/docs/pipeline/nextflow/pipeline-submission/prepare-inputs.md). For miniWDL, the run directory lives under whichever storage mount point you configure (`/fovus-storage` by default) — see [Submit a pipeline (miniWDL)](/docs/pipeline/miniwdl/miniwdl-submission.md). ## What's next?

:bolt: Nextflow quickstart

Run the hello-world example with Fovus-hosted execution.Quickstart

:bolt: miniWDL quickstart

Install miniwdl-fovus and run the hello-world WDL example.Quickstart

:chart-line: Monitor and manage

Track progress, review outputs, and stop or resume Fovus-hosted runs.Monitor & manage
--- # 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/pipeline-overview.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.