gh-k-dense-ai-claude-scientific-skills-scientific-skills/skills/latchbio-integration/references/workflow-creation.md

Workflow Creation and Registration

Overview

The Latch SDK enables defining serverless bioinformatics workflows using Python decorators and deploying them with automatic containerization and UI generation.

Installation

Install the Latch SDK:

python3 -m pip install latch

Prerequisites:

• Docker must be installed and running locally
• Latch account credentials

Initializing a New Workflow

Create a new workflow template:

latch init <workflow-name>

This generates a workflow directory with:

• wf/__init__.py - Main workflow definition
• Dockerfile - Container configuration
• version - Version tracking file

Workflow Definition Structure

Basic Workflow Example

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

@workflow
def my_workflow(input_file: LatchFile, output_dir: LatchDir) -> LatchFile:
    """
    Workflow description that appears in the UI

    Args:
        input_file: Input file description
        output_dir: Output directory description
    """
    return process_task(input_file, output_dir)

Task Definition

Tasks are the individual computation steps within workflows:

from latch import small_task, large_task

@small_task
def process_task(input_file: LatchFile, output_dir: LatchDir) -> LatchFile:
    """Task-level computation"""
    # Processing logic here
    return output_file

Task Resource Decorators

The SDK provides multiple task decorators for different resource requirements:

• @small_task - Default resources for lightweight tasks
• @large_task - Increased memory and CPU
• @small_gpu_task - GPU-enabled tasks with minimal resources
• @large_gpu_task - GPU-enabled tasks with maximum resources
• @custom_task - Custom resource specifications

Registering Workflows

Register the workflow to the Latch platform:

latch register <workflow-directory>

The registration process:

1. Builds Docker container with all dependencies
2. Serializes workflow code
3. Uploads container to registry
4. Generates no-code UI automatically
5. Makes workflow available on the platform

Registration Output

Upon successful registration:

• Workflow appears in Latch workspace
• Automatic UI is generated with parameter forms
• Version is tracked and containerized
• Workflow can be executed immediately

Supporting Multiple Pipeline Languages

Latch supports uploading existing pipelines in:

• Python - Native Latch SDK workflows
• Nextflow - Import existing Nextflow pipelines
• Snakemake - Import existing Snakemake pipelines

Nextflow Integration

Import Nextflow pipelines:

latch register --nextflow <nextflow-directory>

Snakemake Integration

Import Snakemake pipelines:

latch register --snakemake <snakemake-directory>

Workflow Execution

From CLI

Execute a registered workflow:

latch execute <workflow-name> --input-file <path> --output-dir <path>

From Python

Execute workflows programmatically:

from latch.account import Account
from latch.executions import execute_workflow

account = Account.current()
execution = execute_workflow(
    workflow_name="my_workflow",
    parameters={
        "input_file": "/path/to/file",
        "output_dir": "/path/to/output"
    }
)

Launch Plans

Launch plans define preset parameter configurations:

from latch.resources.launch_plan import LaunchPlan

# Define a launch plan with preset parameters
launch_plan = LaunchPlan.create(
    workflow_name="my_workflow",
    name="default_config",
    default_inputs={
        "input_file": "/data/sample.fastq",
        "output_dir": "/results"
    }
)

Conditional Sections

Create dynamic UIs with conditional parameter sections:

from latch.types import LatchParameter
from latch.resources.conditional import conditional_section

@workflow
def my_workflow(
    mode: str,
    advanced_param: str = conditional_section(
        condition=lambda inputs: inputs.mode == "advanced"
    )
):
    """Workflow with conditional parameters"""
    pass

Best Practices

1. Type Annotations: Always use type hints for workflow parameters
2. Docstrings: Provide clear docstrings - they populate the UI descriptions
3. Version Control: Use semantic versioning for workflow updates
4. Testing: Test workflows locally before registration
5. Resource Sizing: Start with smaller resource decorators and scale up as needed
6. Modular Design: Break complex workflows into reusable tasks
7. Error Handling: Implement proper error handling in tasks
8. Logging: Use Python logging for debugging and monitoring

Common Patterns

Multi-Step Pipeline

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

@small_task
def quality_control(input_file: LatchFile) -> LatchFile:
    """QC step"""
    return qc_output

@small_task
def alignment(qc_file: LatchFile) -> LatchFile:
    """Alignment step"""
    return aligned_output

@workflow
def rnaseq_pipeline(input_fastq: LatchFile) -> LatchFile:
    """RNA-seq analysis pipeline"""
    qc_result = quality_control(input_file=input_fastq)
    aligned = alignment(qc_file=qc_result)
    return aligned

Parallel Processing

from typing import List
from latch import workflow, small_task, map_task
from latch.types import LatchFile

@small_task
def process_sample(sample: LatchFile) -> LatchFile:
    """Process individual sample"""
    return processed_sample

@workflow
def batch_pipeline(samples: List[LatchFile]) -> List[LatchFile]:
    """Process multiple samples in parallel"""
    return map_task(process_sample)(sample=samples)

Troubleshooting

Common Issues

1. Docker not running: Ensure Docker daemon is active
2. Authentication errors: Run latch login to refresh credentials
3. Build failures: Check Dockerfile for missing dependencies
4. Type errors: Ensure all parameters have proper type annotations

Debug Mode

Enable verbose logging during registration:

latch register --verbose <workflow-directory>

References

• Official Documentation: https://docs.latch.bio
• GitHub Repository: https://github.com/latchbio/latch
• Slack Community: https://join.slack.com/t/latchbiosdk