FlowDeploy

Getting started

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

Select a pipeline

Connect pipelines through GitHub

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

Try pipeline templates

To help you get started, we have a handful of tested templates for you to try. And you can help others get started by creating your own 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 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 view of a pipeline run, we’ve added a section where you can browse, and download that specific run’s inputs, outputs and data generated by the run.

My drive, buckets, public data

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.

Nextflow

nextflow run hello.nf --profile flowdeploy

Snakemake

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

Monitor pipelines

The web app shows a live stream of both 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, we cache your run intermittently so you don’t have to start the whole run over again.

No vendor lock-in

We use 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 your pipeline progress.

Reduce errors

Our stable infrastructure and tested pipelines reduce both 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