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Currently in Alpha. Install the latest alpha release at latch==2.62.1a2
This feature is undergoing active testing. If you encounter any bugs or issues, please contact our support team at support@latch.bio. Your feedback is invaluable and will directly influence improvements to this feature.
Latch’s Snakemake integration allows developers to build graphical interfaces to expose their Snakemake workflows to wet lab teams. It also provides managed cloud infrastructure to execute, debug, and analyze your workflows. A primary goal for the Snakemake integration is to allow developers to register existing Snakemake projects with minimal added boilerplate and modifications to code.

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How It Works

To get started, install the latest alpha build of latch (Note that the version below may be out of date, please check PyPI for the latest release marked “PRE-RELEASE”): 
pip install latch==2.62.1a2
Next, navigate to your Snakemake workflow directory. Making your pipeline cloud compatible on Latch requires five main steps.
If this is your first time using Latch’s Snakemake integration, we recommend starting with the tutorial, which walks through the process end-to-end. Once you’ve completed it, return to the detailed documentation for each step to deepen your understanding.
1

Define workflow metadata

Specify the parameters you want to expose to scientists on Latch. Documentation ↗
2

Configure resources and containers

Declare the compute specifications and container images for each Snakemake rule. Documentation ↗
3

Use Latch storage in your Snakefile

Configure Snakemake to read and write files directly from Latch Data. Documentation ↗
4

Add an entrypoint

Create a Python file that Latch uses to launch your Snakemake workflow in the cloud. Documentation ↗
5

Write a Dockerfile

Define the environment in which your workflow will run. Documentation ↗
Once these steps are done, you can register this as you would any other Latch workflow: 
$ latch register -y .

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Start Here

To get started, follow along with an example workflow here.
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