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

# Nextflow

> Monitor Nextflow pipelines with Tracer

Tracer integrates with Nextflow to provide step-level visibility into every process and container.<br />
Once installed, it automatically detects all Nextflow processes and displays real-time metrics, performance traces, and cost data for each task.

## Why use Tracer when running Nextflow pipelines

Many teams running Nextflow also rely on Seqera Platform to orchestrate and monitor workflows across different environments.<br />

Because both tools appear in the same setups, we’ve prepared an objective comparison that explains how Tracer and Seqera differ in focus and how they can complement each other effectively.
You can read the full comparison here: [Tracer vs Seqera](/comparisons/Tracer_vs_Seqera)

Nextflow orchestrates complex scientific workflows efficiently, but it doesn’t provide full visibility into why certain tasks run slowly, stall, or waste compute. Tracer fills that gap:

* Real-time insight into every process, container, and tool
* Performance metrics (CPU, memory, I/O, GPU) per task
* Automatic detection of idle or blocked tasks
* AI-native logging for easy debugging and root-cause analysis
* Works across local, HPC, or cloud environments without changes to your Nextflow code

## Getting Started

### Prerequisites

* Nextflow installed and working (`nextflow run hello` test passes)
* Tracer installed on [your operating system](/environments/overview)

### Just run your pipeline, Tracer will automatically attach

If Tracer is already installed on your operating system, you only need to enable the Tracer agent for pipelines that have not been run with Tracer before.<br />
In that case, run the following command:

```bash theme={null}
sudo tracer init --token <your-token>
```

<Info> Go to our [onboarding](https://app.tracer.cloud/dashboard) to get your own personal token</Info>

When running this command, you will be asked to name your pipeline for clear labeling in the dashboard.

## Examples

Launch the Tracer demo workflow:

```bash theme={null}
sudo tracer demo
```

Or run any Nextflow pipeline as usual.

Once the pipeline starts, open the Tracer dashboard, and you’ll see each Nextflow process as a timeline step updating in real time.

<Card href="https://app.tracer.cloud/tracer-bioinformatics">
  <img className="block dark:hidden" src="https://mintcdn.com/tracer/lwvLzCSZlgrNXB_D/images/logo/tracer/Tracer%20Full%20Body%20-%20Black.png?fit=max&auto=format&n=lwvLzCSZlgrNXB_D&q=85&s=3ba40411baa608f2cf09ea4372ad16b2" alt="Tracer Logo" style={{ width: '10%', height: 'auto', marginBottom: '1rem' }} width="311" height="84" data-path="images/logo/tracer/Tracer Full Body - Black.png" />

  <img className="hidden dark:block" src="https://mintcdn.com/tracer/lwvLzCSZlgrNXB_D/images/logo/tracer/Tracer%20Full%20Body%20-%20Black.png?fit=max&auto=format&n=lwvLzCSZlgrNXB_D&q=85&s=3ba40411baa608f2cf09ea4372ad16b2" alt="Tracer Logo" style={{ width: '10%', height: 'auto', marginBottom: '1rem' }} width="311" height="84" data-path="images/logo/tracer/Tracer Full Body - Black.png" />

  <div style={{ fontSize: '1.3rem', fontWeight: '700', marginBottom: '1 rem', color: 'inherit' }}>
    Watch your pipeline run in the Tracer dashboard
  </div>

  <div style={{ color: 'inherit' }}>
    View real-time metrics, resource usage, and performance insights for your pipeline runs.
  </div>
</Card>