Flow Bio Bridge

Flow Bio Bridge

ClawBio's gateway to the Flow.bio platform — browse, search, upload, and launch bioinformatics pipelines on Flow from the command line.

Why This Exists

Flow.bio is a bioinformatics platform hosting curated Nextflow pipelines with managed compute, sample tracking, and collaborative project management. But interacting with Flow requires navigating the web UI or writing custom API scripts.

Flow Bio Bridge makes the platform agent-accessible: authenticate once, then list pipelines, upload samples, launch executions, and poll for results — all from the CLI or via the ClawBio orchestrator.

• Without it: Users must switch between web UI and local analysis, manually track execution IDs, and write one-off upload scripts
• With it: A single CLI covers discovery, upload, execution, and status checking across any Flow instance
• Why ClawBio: Chain Flow pipeline outputs with local ClawBio skills (e.g. Flow RNA-seq → ClawBio diffviz)

Core Capabilities

1. Authentication — Login via username/password, existing JWT token, or environment variables
2. Pipeline discovery — List and inspect available Nextflow pipelines with versions and parameter schemas
3. Sample management — List, search, and upload samples with metadata and organism tagging
4. Project browsing — List owned/shared projects and their contents
5. Execution tracking — Launch pipeline runs, poll status, and retrieve logs
6. Search — Full-text search across samples, projects, data, and executions
7. Data listing — Browse owned and shared data files
8. Organism & type discovery — List available organisms and sample types for uploads
9. Overview mode — Live overview of any Flow instance; public data without credentials, full account view with login

Input Formats

Workflow

When the user asks to interact with Flow.bio:

1. Authenticate: Use stored token, env vars, or prompt for credentials
2. Discover: List pipelines, sample types, organisms as needed