latchbio-integration

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

# 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

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

@small_task
def process_file(input_file: LatchFile) -> LatchFile:
    """Process a single file"""
    # Processing logic
    return output_file

@workflow
def my_workflow(input_file: LatchFile) -> LatchFile:
    """
    My bioinformatics workflow

    Args:
        input_file: Input data file
    """
    return process_file(input_file=input_file)