latchbio-integration

# 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:

| Need | Reference |
|---|---|
| Python workflows, tasks, maps, conditions, caching | `references/workflow-creation.md` |
| `LPath`, legacy file types, Latch URLs, data CLI | `references/data-management.md` |
| Registry reads, transactions, samplesheets | `references/registry.md` |
| CPU, memory, storage, GPU, dynamic resources | `references/resource-configuration.md` |
| Nextflow and Snakemake packaging | `references/nextflow-snakemake.md` |
| Metadata, forms, launch plans, messages, automations | `references/ui-and-automation.md` |
| Registration, development, execution, monitoring | `references/operations-and-debugging.md` |
| Ready-to-use workflows and `latch.verified` | `references/verified-workflows.md` |
| Remote MCP setup and tool workflow | `references/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.

## 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 2.76.8, 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 li