ContextQMD
Back to Claude Scientific Skills

LatchBio Integration

skills/latchbio-integration/SKILL.md

2.55.07.6 KB
Original Source

LatchBio Integration

Current Baseline

This skill targets Latch SDK 2.76.8, released July 10, 2026. The package metadata supports Python 3.9–3.12 and declares Python 3.9+.

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:

NeedReference
Python workflows, tasks, maps, conditions, cachingreferences/workflow-creation.md
LPath, legacy file types, Latch URLs, data CLIreferences/data-management.md
Registry reads, transactions, samplesheetsreferences/registry.md
CPU, memory, storage, GPU, dynamic resourcesreferences/resource-configuration.md
Nextflow and Snakemake packagingreferences/nextflow-snakemake.md
Metadata, forms, launch plans, messages, automationsreferences/ui-and-automation.md
Registration, development, execution, monitoringreferences/operations-and-debugging.md
Ready-to-use workflows and latch.verifiedreferences/verified-workflows.md
Remote MCP setup and tool workflowreferences/latch-mcp.md

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:

bash
uv venv --python 3.12
source .venv/bin/activate
uv pip install "latch==2.76.8"

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:

bash
latch login
latch workspace

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

bash
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:

bash
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.

python
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:
    """Return the reverse complement of a DNA sequence."""
    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.

  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 2.76.8, the staging branch does not generate one from --nf-script or --snakefile.

    bash
    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

    bash
    latch register --yes --open .

    Useful controls:

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

    Duplicate registration exits with status 2; it is not the same as a build failure.

  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.

Operational Safety

  • Ask for confirmation before launching paid compute, especially GPU or large batch runs.
  • Ask for confirmation before LPath.rmr, latch rmr, Registry deletion, or overwriting shared destinations.
  • Never log secrets, SDK tokens, signed URLs, or secret values.
  • Call get_secret() only inside a task, use the returned value only for its intended service, and never return it as workflow output.
  • Do not pass untrusted strings through shell commands. Prefer argument lists with subprocess.run(..., check=True).
  • Pin the SDK and workflow dependencies for releases. Upgrade only after reviewing the changelog and re-running staging tests.
  • Treat generated files as generated: customize the documented extension file rather than editing output that the CLI will overwrite.

Inspect the Installed SDK

From this skill directory:

bash
uv run --no-project --python 3.12 --with "latch==2.76.8" \
  python scripts/inspect_latch_sdk.py

Use JSON output for automated comparisons:

bash
uv run --no-project --python 3.12 --with "latch==2.76.8" \
  python scripts/inspect_latch_sdk.py --json

Authoritative Sources