Run bioinformatics pipelines in the cloud using Snakemake or Nextflow.
Bioinformaticians use FlowDeploy to try, run and develop pipelines.
Getting started
Try, run, and develop bioinformatic pipelines with a bit of help from FlowDeploy.

Select a pipeline

Connect pipelines through GitHub

Import custom and public pipelines through GitHub. The git branches and releases are automatically imported and refreshed.

Try pipeline templates

To help you get started, FlowDeploy has a handful of tested templates for you to try. And you can help others get started by creating your own templates.

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flowdeploy run acme/rnaseq -v "1.1.0"

Choose how you run pipelines

Using our web app

Start running pipelines right away on your browser, with no installation needed.

Programmatically with the FlowDeploy API

Build your own framework around FlowDeploy to run and manage your pipelines. After launch, you will be able to monitor your pipelines through the web app.

Manage your pipeline data

Inputs, outputs, run data

On the web app, you can browse and download the inputs, outputs and data generated by a pipeline run.

My drive, buckets, public data

Manage files in your FlowDeploy drive, connect S3 buckets and leverage public data.

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nextflow run --profile flowdeploy
snakemake --rerun-incomplete --profile flowdeploy

Flexibly develop your pipelines

On your own infrastructure

Continue to develop pipelines on your laptop, server, or a cloud.

With the help of FlowDeploy for more intensive steps

You can run individual steps with FlowDeploy while running on your own infrastructure.

Reach milestones faster
FlowDeploy works with you, so you can get your results quickly.
See what we're talking about
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Monitor pipelines
The web app has a live stream of the run logs, pipeline steps, and resource usage. You can also browse through files as they are created by the run.
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Avoid lengthy restarts
Like a “checkpoint” in a video game, your run is cached intermittently so you don’t have to start the whole run over again.
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No vendor lock-in
FlowDeploy uses an open source bioinformatics task execution protocol, managed by an independent non-profit.
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Live updates with Slack webhook
Receive push notifications from Slack to track pipeline progress.
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Reduce errors
Stable infrastructure and tested pipelines reduce pipeline and operational errors.
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Team based auth
Securely manage your team through FlowDeploy, or integrate your existing user permissions with SSO.


Nextflow vs snakemake

Nextflow vs. Snakemake

How do you choose between Nextflow and Snakemake when writing a bioinformatics pipeline?

Learn more
Airflow vs Snakemake

Airflow vs. Snakemake

What are the pros and cons of these two python based workflow managers for bioinformatics?

Learn more
A purple rocketship

Starting a bioinformatics team

A guide for people with technical experience in bioinformatics, who have never built their own team.

Show me the guide
Books and tea

Read the docs

Everything you need to know about FlowDeploy and how you can use it.

The docs
Run a pipeline
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