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Develop a pipeline

Using FlowDeploy to assist with local pipeline development.


Some people don't need FlowDeploy develop mode! Develop mode is helpful for augmenting development your own computer with cloud resources for intensive steps.

After choosing an open-source pipeline – or starting from scratch – you can use FlowDeploy to develop on your own computer and selectively use the cloud for intensive steps.

This is useful if you want to test an intensive step – like alignment – that needs hundreds of gigabytes of memory, but you aren't ready to deploy a pipeline.

With Nextflow

  1. Install Nextflow, if you haven't already.

  2. Connect your device to FlowDeploy.


Develop mode might be disabled on your account. Contact your administrator or the FlowDeploy team for help.

  1. Clone the "Hello world!" project:
git clone nextflow-io/hello
  1. Edit line 11 of "" in the project to say "FlowDeploy" instead of "world"

  2. Run nextflow on the command-line, using demo data for this tutorial:

nextflow run nextflow-io/hello --pipeline --profile flowdeploy,docker
  1. You're running the custom pipeline tasks in the cloud through FlowDeploy! You can observe the run from either your computer or the FlowDeploy app.