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Run an open-source pipeline

Running an open-source pipeline with FlowDeploy.

Let's run the simple Nextflow pipeline to fetch NGS data, nf-core/fetchngs.

In your browser​

Try the pre-populated nf-core/fetchngs 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.nextflow():
import flowdeploy

flowdeploy.set_key("YOUR_KEY")
flowdeploy.nextflow(
    pipeline="nf-core/fetchngs",
    pipeline_version="1.10.0",
    outdir="fd://YOUR_HOME/tutorial_one/",
    profiles=["docker", "test"],
)

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

You can follow the pipeline's execution in your browser.

On the command line​

If you haven't already, make sure to:

  • Install pip (or pipx)
  • Sign up for FlowDeploy, and create a new key
  1. Install the FlowDeploy CLI and Python package:
pip install flowdeploy
  1. Set your key and call flowdeploy run
flowdeploy set-key YOUR_KEY
flowdeploy run nextflow nf-core/fetchngs --version 1.10.0 --outdir fd://YOUR_HOME/tutorial_one --profile docker --profile test

That's it! Run the command, and the pipeline runs in FlowDeploy! 🎉