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Introducing nf-core pipelines on Code Ocean

nf-core pipelines are now available on the latest Code Ocean release (2.19). Here, we will share insights into what nf-core is, why it matters, how it works, and how you can use them in your bioinformatics workflows. 

What is nf-core?

nf-core is a community-created collection of open-source bioinformatics pipelines written in Nextflow. Considered by many to be the industry standard DSL for scientific workflow management, it offers almost 60 pipelines including:

  • rnaseq: RNA sequencing using STAR, RSEM, and HISAT2/Salmon
  • sarek: for the detection of germline or somatic variants
  • mag: for assembly, binning, and annotation of metagenomes 
  • chipseq: for processing Chromatin ImmunopreciPitation sequencing data
  • scrnaseq: for processing 10x Genomics single-cell RNA-seq data
  • atacseq: for the analysis of ATAC-seq data

Solving common computational challenges with nf-core pipelines on Code Ocean

The #1 goal of this release is to solve the challenges that come with installing, configuring, and running nf-core pipelines, like command line expertise, reviewing extensive documentation, and the inevitable troubleshooting that comes into play. 

Based on a webinar survey, we learned that over 85% of respondents feel that they’re spending too much time troubleshooting when using nf-core pipelines, which is why we’ve been so eager to share this release!

We solve this by doing all of the installation and configuration for you. You choose the pipeline, we install, then you click RUN. 

Why do nf-core pipelines on Code Ocean matter? 

nf-core pipelines are open source and free to use, but they’re out of reach to anyone who doesn’t know Nextflow or how to provision cloud compute to run them (e.g. AWS Batch). Code Ocean automates many of these steps and adds additional benefits:

  • Provision compute: run nf-core pipelines on AWS EC2 without additional config
  • Attach data of any size: straightforward parameterization lets you attach and process any of your cloud data
  • Prove result lineage: the Lineage Graph shows all result provenance with a single click
  • Reproduce results: results generated within Code Ocean are guaranteed to be reproducible

How do nf-core pipelines work on Code Ocean? 

nf-core pipelines import and install on Code Ocean with a simple dropdown:

You can then begin immediately defining the pipeline’s parameters, e.g.:

For compute, the pipeline will run either with On Demand EC2 instances or spot instances depending on your preference, and with or without the cache from any previous run:

Once all of this is set up, the pipeline is ready to run.

How to get started with nf-core pipelines on Code Ocean

If you’re already a Code Ocean customer, make sure you’re upgraded to 2.19. The option to use nf-core pipelines will be available from the Pipelines dashboard in the top right corner:

If you’re not a Code Ocean customer and want to learn more, you can watch a full demo of nf-core pipelines on Code Ocean at 10:15 in the video above. 


Alicia Liu

Product Manager

Alicia Liu

Product Manager

Alicia Liu

Alicia is a Product Manager at Code Ocean. She received her Ph.D. in molecular and cell biology, and conducted research in the area of epigenetics and genomic imprinting. Before joining Code Ocean, she supported biopharma and biotech customers with their NGS projects at Azenta Life Sciences.