latchbio-integration

Files (11)

• SKILL.md
• data-management.md · references/
• latch-mcp.md · references/
• nextflow-snakemake.md · references/
• operations-and-debugging.md · references/
• registry.md · references/
• resource-configuration.md · references/
• ui-and-automation.md · references/
• verified-workflows.md · references/
• workflow-creation.md · references/
• inspect_latch_sdk.py · scripts/

SKILL.md (first lines)

# 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:

| 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==2.77.1"
```

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:

```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:
    """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,

From K-Dense-AI/scientific-agent-skills, MIT.

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