/latchbio-integration

name: latchbio-integration
description: Latch platform for bioinformatics workflows. Build pipelines with Latch SDK, @workflow/@task decorators, deploy serverless workflows, LatchFile/LatchDir, Nextflow/Snakemake integration.
license: Unknown
metadata:
    skill-author: K-Dense Inc.

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)

When to Use This Skill

This skill should be used when encountering any of the following scenarios:

**Workflow Development:**

• "Create a Latch workflow for RNA-seq analysis"
• "Deploy my pipeline to Latch"
• "Convert my Nextflow pipeline to Latch"
• "Add GPU support to my workflow"
• Working with `@workflow`, `@task` decorators

**Data Management:**

• "Organize my sequencing data in Latch Registry"
• "How do I use LatchFile and LatchDir?"
• "Set up sample tracking in Latch"
• Working with `latch:///` paths

**Resource Configuration:**

• "Configure GPU for AlphaFold on Latch"
• "My task is running out of memory"
• "How do I optimize workflow costs?"
• Working with task decorators

**Verified Workflows:**

• "Run AlphaFold on Latch"
• "Use DESeq2 for differential expression"
• "Available pre-built workflows"
• Using `latch.verified` module

Detailed Documentation

This skill includes comprehensive reference documentation organized by capability:

references/workflow-creation.md

**Read this for:**

• Creating and registering workflows
• Task definition and decorators
• Supporting Python, Nextflow, Snakemake
• Launch plans and conditional sections
• Workflow execution (CLI and programmatic)
• Multi-step and parallel pipelines
• Troubleshooting registration issues

**Key topics:**

• `latch init` and `latch register` commands
• `@workflow` and `@task` decorators
• LatchFile and LatchDir basics
• Type annotations and docstrings
• Launch plans with preset parameters
• Conditional UI sections

references/data-management.md

**Read this for:**

• Cloud storage with LatchFile and LatchDir
• Registry system (Projects, Tables, Records)
• Linked records and relationships
• Enum and typed columns
• Bulk operations and transactions
• Integration with workflows
• Account and workspace management

**Key topics:**

• `latch:///` path format
• File transfer and glob patterns
• Creating and querying Registry tables
• Column types (string, number, file, link, enum)
• Record CRUD operations
• Workflow-Registry integration

references/resource-configuration.md

**Read this for:**

• Task resource decorators
• Custom CPU, memory, GPU configuration
• GPU types (K80, V100, A100)
• Timeout and storage settings
• Resource optimization strategies
• Cost-effective workflow design
• Monitoring and debugging

**Key topics:**

• `@small_task`, `@large_task`, `@small_gpu_task`, `@large_gpu_task`
• `@custom_task` with precise specifications
• Multi-GPU configuration
• Resource selection by workload type
• Platform limits and quotas

references/verified-workflows.md

**Read this for:**

• Pre-built production workflows
• Bulk RNA-seq and DESeq2
• AlphaFold and ColabFold
• Single-cell analysis (ArchR, scVelo)
• CRISPR editing analysis
• Pathway enrichment
• Integration with custom workflows

**Key topics:**

• `latch.verified` module imports
• Available verified workflows
• Workflow parameters and options
• Combining verified and custom steps
• Version management

Common Workflow Patterns

Complete RNA-seq Pipeline

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

@small_task
def quality_control(fastq: LatchFile) -> LatchFile:
    """Run FastQC"""
    return qc_output

@large_task
def alignment(fastq: LatchFile, genome: str) -> LatchFile:
    """STAR alignment"""
    return bam_outp