latchbio-integration

What this skill does

# 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

@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

```python
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_output

@small_task
def quantification(bam: LatchFile) -> LatchFile:
    """featureCounts"""
    return counts

@workflow
def rnaseq_pipeline(
    input_fastq: LatchFile,
    genome: str,
    output_dir: LatchDir
) -> LatchFile:
    """RNA-seq analysis pipeline"""
    qc = quality_control(fastq=input_fastq)
    aligned = alignment(fastq=qc, genome=genome)
    return quantification(bam=aligned)
```

### GPU-Accelerated Workflow

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

@small_task
def preprocess(input_file: LatchFile) -> LatchFile:
    """Prepare data"""
    return processed

@large_gpu_task
def gpu_computation(data: LatchFile) -> LatchFile:
    """GPU-accelerated analysis"""
    return results

@workflow
def gpu_pipeline(input_file: LatchFile) -> LatchFile:
    """Pipeline with GPU tasks"""
    preprocessed = preprocess(input_file=input_file)
    return gpu_computation(data=preprocessed)
```

### Registry-Integrated Workflow

```python
from latch import workflow, small_task
from latch.registry.table import Table
from latch.registry.record import Record
from latch.types import LatchFile

@small_task
def process_and_track(sample_id: str, table_id: str) -> str:
    """Process sample and update Registry"""
    # Get sample from registry
    table = Table.get(table_id=table_id)
    records = Record.list(table_id=table_id, filter={"sample_id": sample_id})
    sample = records[0]

    # Process
    input_file = sample.values["fastq_file"]
    output = process(input_file)

    # Update registry
    sample.update(values={"status": "completed", "result": output})
    return "Success"

@workflow
def registry_workflow(sample_id: str, table_id: str):
    """Workflow integrated with Registry"""
    return process_and_track(sample_id=sample_id, table_id=table_id)
```

## Best Practices

### Workflow Design
1. Use type annotations for all parameters
2. Write clear docstrings (appear in UI)
3. Start with standard task decorators, scale up if needed
4. Break complex workflows into modular tasks
5. Implement proper error handling

### Data Management
6. Use consistent folder structures
7. Define Registry schemas before bulk entry
8. Use linked records for relationships
9. Store metadata in Registry for traceability