FlowDeploy

Getting started

Try, run, and develop bioinformatic pipelines with a bit of help from FlowDeploy.

Try pipelines

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 to try and use. You can also help others get started by creating your own pipeline templates.

Shell

flowdeploy run acme/rnaseq -v "1.1.0"

Python

flowdeploy.snakemake(  pipeline="acme/rnaseq",  pipeline_version="1.1.0",  profiles=["docker"],  use_git_release=True 

)

Choose how you run pipelines

Using our web app

Start running custom or public 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, monitor pipelines through the web app.

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

Run individual steps with FlowDeploy while running the pipeline on your own infrastructure.

Nextflow

nextflow run hello.nf --profile flowdeploy

Snakemake

snakemake --rerun-incomplete --profile flowdeploy

Reach milestones faster

FlowDeploy works with you, so you can get your results quickly.

See what we're talking about

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.

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.

No vendor lock-in

FlowDeploy uses an open source bioinformatics task execution protocol, managed by an independent non-profit.

Live updates with Slack webhook

Receive push notifications from Slack to track pipeline progress.

Reduce errors

Stable infrastructure and tested pipelines reduce pipeline and operational errors.

Team based auth

Securely manage your team through FlowDeploy, or integrate your existing user permissions with SSO.

Resources

Nextflow vs. Snakemake

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

Learn more

Airflow vs. Snakemake

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

Learn more

Starting a bioinformatics team

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

Show me the guide

Read the docs

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

The docs