# Flow Bio

Flow.bio API bridge, authenticate, browse pipelines/samples/projects, search, upload...

- Repository: https://github.com/ClawBio/ClawBio (1172 stars)
- Category: Engineering
- License: MIT
- Last updated: 2026-11-01
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add ClawBio/ClawBio --skill flow-bio -g -a claude-code -y`
Codex: `npx skills add ClawBio/ClawBio --skill flow-bio -g -a codex -y`
Cursor: `npx skills add ClawBio/ClawBio --skill flow-bio -g -a cursor -y`
Gemini CLI: `npx skills add ClawBio/ClawBio --skill flow-bio -g -a gemini-cli -y`
Claude Code plugin marketplace: `/plugin marketplace add ClawBio/ClawBio`

## Description

Flow.bio API bridge, authenticate, browse pipelines/samples/projects, search, upload data, launch pipeline executions, and check run status on any Flow instance.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# 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

The rest: https://github.com/ClawBio/ClawBio/blob/HEAD/skills/flow-bio/SKILL.md