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

2. Data Management

3. Resource Configuration

4. Verified Workflows

Quick Start

Installation and Setup

# Install Latch SDK
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:

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:

Data Management:

Resource Configuration:

Verified Workflows:

Detailed Documentation

This skill includes comprehensive reference documentation organized by capability:

references/workflow-creation.md

Key topics:

references/data-management.md

Key topics:

references/resource-configuration.md

Key topics:

references/verified-workflows.md

Key topics:

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_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

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

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

Data Management

Resource Configuration

Development Workflow

Troubleshooting

Common Issues

Registration Failures:

Resource Problems:

Data Access:

Type Errors:

Additional Resources

Support

For issues or questions: