> ## Documentation Index
> Fetch the complete documentation index at: https://docs.biomni.phylo.bio/llms.txt
> Use this file to discover all available pages before exploring further.

# Pipelines

> Prepare, run, and review scientific workflows with Nextflow

Pipelines run a defined series of analysis steps across samples. Biomni can help
prepare inputs and interpret results, while **Nextflow** coordinates the
workflow on managed cloud compute.

Phylo supports selected versioned pipelines from the [nf-core
community](https://nf-co.re/) and compatible custom Nextflow workflows. Open
**Resources** from the main navigation, select **Tools**, then choose the
**Nextflow** filter to browse established pipelines available in your workspace.

## Prepare a run

In a task, add a pipeline from **+ Add → Resources** and reference your input
files with `@`. Ask Biomni to check the inputs and configuration. For example:

```text theme={null}
Prepare an nf-core/rnaseq run for these files. Check sample matching and
parameters, then show me the configuration before starting.
```

Before launch, review that:

* the pipeline matches your analysis;
* samples and metadata are correct; and
* references and parameters fit your study.

You can also provide a custom workflow. Include its `main.nf`, required modules
or config files, and input data. Ask Biomni to check the files and explain the
workflow's expected inputs and outputs.

## Monitor and review

In the task, you can follow:

* overall and process-level progress;
* logs and error details; and
* reports and outputs when available.

If a run fails, ask Biomni to explain the error and suggest a next step. You may
be able to resume completed work or need to correct the inputs and run again.

Review completed outputs alongside the scientific results. Run details and
output lineage can help identify which process produced a file. Keep the
pipeline version, inputs, references, and parameters with your analysis.

To explore the run lifecycle without your own sequencing files, ask Biomni to
use the `nf-core/rnaseq` test profile:

```text theme={null}
Run nf-core/rnaseq with its test profile. Show me the configuration before
launching, then summarize the run and outputs.
```

Check that the method and parameters fit your research question. Validate new
or modified workflows on representative data. Biomni can help prepare and
interpret a run, but researchers remain responsible for reviewing the method
and results.

[Nextflow](https://www.nextflow.io/) is an open-source workflow system developed
by [Seqera](https://seqera.io/) and its contributor community. Biomni supports
Nextflow and selected [nf-core](https://nf-co.re/) pipelines. Phylo and Biomni
are independent products and are not affiliated with, sponsored by, or endorsed
by Seqera or nf-core.


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