Latchbio Integration

LatchBio Integration

Current Baseline

This skill targets Latch SDK 2.77.1, released September 17, 2026. The package metadata supports Python 3.9–3.12 and declares Python 3.9+.

Review status: the SDK imports, documented signatures, CLI help, and selected workflow graph examples were checked locally with Python 3.12. Network-backed examples are illustrative: no authenticated registration, data mutation, launch, or MCP tool call was performed during this refresh.

Treat the installed package and its changelog as authoritative when a guide disagrees with the SDK. Some Latch guides retain older Python ranges or compatibility-specific pre-release pins, especially the Snakemake v2 tutorial. Never combine commands or imports from different tracks without checking their version requirements.

When to Use

Use this skill to:

• Create or maintain Python SDK workflows and task graphs
• Package and register Python, Nextflow, or Snakemake pipelines
• Configure task CPU, memory, storage, GPU, caching, retries, and timeouts
• Work with Latch Data through LPath, LatchFile, LatchDir, or the CLI
• Read or update Latch Registry projects, tables, and records
• Design workflow forms, launch plans, samplesheets, messages, and result links
• Stage and debug workflow images with latch register --staging and latch develop
• Launch and monitor workflows through Python or Latch MCP
• Discover and use ready-to-run Latch workflows

Route to the Right Reference

Read only the references needed for the task:

Before relying on a symbol, run scripts/inspect_latch_sdk.py against the target SDK version. It performs local imports only and does not authenticate or make network requests.

Installation and Authentication

For a reproducible environment:

uv venv --python 3.12
source .venv/bin/activate
uv pip install "latch==2.77.1"

On Windows, use WSL for the documented Linux workflow tooling.

Authenticate through the supported OAuth flow; do not read, print, copy, or parse ~/.latch/token manually:

latch login
latch workspace

Select a workspace non-interactively when its numeric ID is already known:

latch workspace --id 12345

latch login credentials are for the SDK and CLI. Latch MCP uses a separate OAuth authorization and its credentials cannot be reused for general SDK access.

Fast Path

Create and remotely register the maintained subprocess template:

latch init covid-wf --template subprocess
latch register --yes --open covid-wf

Remote image building is the default. Use --no-remote only when a local Docker daemon is available and a local build is intentional.

Minimal Python Workflow

Keep workflow bodies declarative: invoke tasks and return their promises. Perform computation and side effects inside tasks.

from latch import small_task, workflow


@small_task
def reverse_complement(sequence: str) -> str:
    table = str.maketrans("ACGTacgt", "TGCAtgca")
    return sequence.translate(table)[::-1]


@workflow
def reverse_complement_workflow(sequence: str) -> str:
    """Reverse-complement a DNA sequence.

    This minimal example handles A, C, G, and T bases.
    """
    return reverse_complement(sequence=sequence)

Use @workflow(metadata) when the generated interface needs custom labels, sections, validation rules, samplesheets, or documentation links. Use LatchFile or LatchDir for automatic task input staging and output upload; use LPath for imperative remote path operations.

Recommended Development Lifecycle

1. Inspect compatibility

   • Confirm the installed SDK and Python version.
   • Identify whether the project is Python, Nextflow, the legacy Snakemake flag path, or the separately pinned Snakemake v2 tutorial track.

2. Define a typed interface

   • Annotate every workflow and task input and output.
   • Keep module import time free of network calls, data mutations, and secret retrieval. Isolate documented exceptions such as workflow_reference, which resolves the active workspace when its decorator is evaluated.
   • Use dataclasses and enums for structured parameters.

3. Configure metadata and resources

   • Match metadata parameter keys to the workflow signature.
   • Start with named task decorators, then use custom_task only when measured requirements justify it.

4. Validate in the execution image

   Fresh Nextflow and Snakemake projects must generate their version-compatible Python entrypoint before staging. In SDK 2.77.1, the staging branch does not generate one from --nf-script or --snakefile.

   latch register --staging .
   latch develop .

   Re-run staging registration after changing the Dockerfile or dependencies. Edits made inside the development container are not synced back.

5. Register deliberately

   latch register --yes --open .

   Useful controls:

   latch register --workspace-id 12345 .
   latch register --mark-as-release .
   latch register --workflow-module wf.custom_entrypoint .

   Ordinary duplicate registration exits with status 2; duplicate staging registration exits with status 1. Staging uses the active workspace and does not honor --workspace-id; select it with latch workspace --id first.

6. Launch only after reviewing cost and parameters

   • Prefer the Console or Latch MCP for interactive operation.
   • Prefer latch_cli.services.launch.launch_v2 for Python automation.
   • Do not use the deprecated latch launch CLI as a new integration pattern.

7. Monitor and verify

   • Check terminal status, task logs, result links, and scientific outputs.
   • Treat successful orchestration as necessary but not sufficient scientific validation.