canonical: https://jentic.com/apis/illumina.com/illuminaconnectedanaly

# Illumina Connected Analytics API

Illumina Connected Analytics is a genomics analysis platform API for running bioinformatics pipelines in the cloud. It starts CWL and Nextflow pipeline executions within a project, lists analyses and fetches their outputs, and reports the available analysis storage options. Projects, pipelines, and external storage credentials are managed through the same interface, giving genomics teams programmatic control over large-scale sequencing analysis.

## For AI agents

Lets an AI agent launch CWL and Nextflow genomics pipelines on Illumina Connected Analytics, track analyses within a project, and download their outputs.

## Scope

Does not handle sequencing instrument control, variant interpretation, or clinical reporting. Use it for launching and retrieving genomics pipeline analyses only.

## Capabilities

- List genomics projects and their available storage options
- Start CWL pipeline executions within a project
- Start Nextflow pipeline executions within a project
- Retrieve analyses and download their outputs
- Register external storage credentials for analysis data
- Manage pipeline lifecycle including archive and deprecation

## Use cases

### Cloud genomics pipeline execution

A bioinformatics team needs to run CWL or Nextflow pipelines on sequencing data without managing its own compute. Illumina Connected Analytics launches a pipeline within a project, tracks the resulting analysis, and exposes the outputs for retrieval, so a team can move from a dataset to results through the interface. Storage options are reported per analysis.

Example prompt: Start a Nextflow pipeline execution in a project and record the returned analysis identifier

### Analysis output retrieval

Downstream tools need the files a pipeline produced. The API lists the analyses in a project and fetches the outputs for a completed run, letting a workflow collect result files as soon as an analysis finishes. Listing is paginated so large projects can be walked in order.

Example prompt: List completed analyses in a project and fetch the outputs for the most recent one

### AI agent genomics workflow

An AI agent coordinating a genomics workflow can launch a pipeline, poll for completion, and gather outputs without manual steps. The agent selects the project, starts the CWL or Nextflow run, and retrieves results, with pipeline launches gated behind operations the lab has allowed. Read-only listing keeps monitoring separate from execution rights.

Example prompt: Given a project and pipeline, start the analysis, wait for completion, and download its outputs

## Key endpoints

| Method | Path | Description |
| --- | --- | --- |
| GET | `/projects` | List projects |
| POST | `/projects/{projectId}/analysis:cwl` | Start a CWL pipeline execution |
| POST | `/projects/{projectId}/analysis:nextflow` | Start a Nextflow pipeline execution |
| GET | `/projects/{projectId}/analyses` | List analyses in a project |
| GET | `/projects/{projectId}/analyses/{analysisId}/outputs` | Fetch analysis outputs |
| GET | `/analysisStorages` | List available analysis storage options |

## Key resources

- **Projects** — List projects and their analyses with cursor and offset pagination
- **Analysis** — Start CWL and Nextflow pipeline executions and fetch analysis outputs
- **Pipelines** — Manage pipeline lifecycle including archive and deprecation
- **Storage** — Report analysis storage options and register external storage credentials

## Why Jentic

- **Setup:** Wiring Illumina Connected Analytics by hand means provisioning an API key, learning the project-scoped analysis paths, and building the CWL and Nextflow launch payloads. Install Jentic One once, import the API from the Jentic API Directory, and store the credential once for your agent to reuse.
- **Permission scoping:** Scope your agent to read-only operations such as listing projects and fetching outputs, and, because the project is a path parameter on the analysis operations, restrict it to a single project. You decide which operations are callable.
- **Credential handling:** Your Illumina API key is stored once, encrypted, by your own Jentic One instance and injected only at execution time. It never enters the agent's prompt, logs, or context.
- **Discovery method:** Agents find Illumina Connected Analytics through Jentic's intent search: a query such as 'run a genomics pipeline' matches the analysis and project operations, which the agent then calls with your stored credential.

## Related APIs

- **Google Cloud Life Sciences** — Managed execution of genomics and life-science pipelines on Google Cloud
- **AWS** — Cloud compute and storage services for large data workloads
- **Google Cloud Storage** — Object storage for input datasets and analysis outputs

## FAQ

### What can an AI agent do with the Illumina Connected Analytics API?

An agent can list projects and storage options, start CWL and Nextflow pipeline executions within a project, list analyses, and download the outputs of a completed run. It covers launching and retrieving genomics analyses.

### How does the Illumina Connected Analytics API authenticate?

It authenticates with an API key sent in an X-API-Key header on each request. Jentic injects the key at execution time so it stays out of the agent's context.

### Can I limit what my agent is allowed to do with the Illumina Connected Analytics API?

Yes. Your Jentic One instance decides which operations an agent may call, so you can allow read-only listing and output retrieval while withholding pipeline launches. Because the project is a path parameter, you can also confine an agent to a single project.

### Which pipeline languages does the platform run?

It runs both CWL and Nextflow pipeline executions within a project, and returns the resulting analyses and their outputs for download once a run completes.

### How do I connect the Illumina Connected Analytics API to my AI agent with Jentic?

Install Jentic One with its setup script, import the API from the Jentic API Directory, and store your API key once. Your agent can then call the project, analysis, and output operations you allow.