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Run a Snakemake Workflow

Run an open-source Snakemake Workflow with FlowDeploy.

Let's run a simple Snakemake pipeline, based on the Snakemake tutorial.

In your browser​

Try the pre-populated snakemake-demo example

In Python​

If you haven't already, make sure to:

  • Install Python 3.9 or above
  • Sign up for FlowDeploy, and create a new key
  1. Install the FlowDeploy Python package.
$ pip install flowdeploy
  1. In Python, set your key and call flowdeploy.snakemake():
import flowdeploy

flowdeploy.set_key("YOUR_KEY")
flowdeploy.snakemake(
    targets=["results/mapped/A.bam"],
    pipeline='trytoolchest/snakemake-demo',
    pipeline_version='v0.1.0',
    run_location=f'fd://shared/',
    snakemake_folder='snakemake-demo', 
    cli_args='--use-conda',
)

That's it! Execute your code, and the pipeline runs in FlowDeploy! 🎉

You can follow the pipeline's execution in the FlowDeploy app.