# Latchbio Integration

Latch platform for bioinformatics workflows.

- Repository: https://github.com/synthetic-sciences/openscience (4321 stars)
- Category: DevOps
- License: Unknown
- Last updated: 2026-10-30
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add synthetic-sciences/openscience --skill latchbio-integration -g -a claude-code -y`
Codex: `npx skills add synthetic-sciences/openscience --skill latchbio-integration -g -a codex -y`
Cursor: `npx skills add synthetic-sciences/openscience --skill latchbio-integration -g -a cursor -y`
Gemini CLI: `npx skills add synthetic-sciences/openscience --skill latchbio-integration -g -a gemini-cli -y`

## Description

Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.

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

# LatchBio Integration

## Overview

Latch is a Python framework for building and deploying bioinformatics workflows as serverless pipelines. Built on Flyte, create workflows with @workflow/@task decorators, manage cloud data with LatchFile/LatchDir, configure resources, and integrate Nextflow/Snakemake pipelines.

## Core Capabilities

The Latch platform provides four main areas of functionality:

### 1. Workflow Creation and Deployment
- Define serverless workflows using Python decorators
- Support for native Python, Nextflow, and Snakemake pipelines
- Automatic containerization with Docker
- Auto-generated no-code user interfaces
- Version control and reproducibility

### 2. Data Management
- Cloud storage abstractions (LatchFile, LatchDir)
- Structured data organization with Registry (Projects → Tables → Records)
- Type-safe data operations with links and enums
- Automatic file transfer between local and cloud
- Glob pattern matching for file selection

### 3. Resource Configuration
- Pre-configured task decorators (@small_task, @large_task, @small_gpu_task, @large_gpu_task)
- Custom resource specifications (CPU, memory, GPU, storage)
- GPU support (K80, V100, A100)
- Timeout and storage configuration
- Cost optimization strategies

### 4. Verified Workflows
- Production-ready pre-built pipelines
- Bulk RNA-seq, DESeq2, pathway analysis
- AlphaFold and ColabFold for protein structure prediction
- Single-cell tools (ArchR, scVelo, emptyDropsR)
- CRISPR analysis, phylogenetics, and more

## Quick Start

### Installation and Setup

```bash
# Install Latch SDK
python3 -m uv pip install latch

# Login to Latch
latch login

# Initialize a new workflow
latch init my-workflow

# Register workflow to platform
latch register my-workflow
```

**Prerequisites:**
- Docker installed and running
- Latch account credentials
- Python 3.8+

### Basic Workflow Example

```python
from latch import workflow, small_task
from latch.types import LatchFile

The rest: https://github.com/synthetic-sciences/openscience/blob/HEAD/backend/cli/skills/biology/latchbio-integration/SKILL.md