Evan Floden
Evan FlodenMay 23, 2024

Empowering scientists with seamless access to bioinformatics resources

Seqera is built on the promise that modern tooling and open software can improve scientists’ daily lives. We believe in empowering scientists and developers to focus on what they do best: groundbreaking research. Today marks a major milestone in that journey as we release two new free and open resources for the community: Seqera Pipelines and Seqera Containers.

These projects bring together the components bioinformaticians need into a simple interface, making it easy to find open-source pipelines to run or build a software container combining virtually any tools. By streamlining access to resources and fostering collaboration, we improve the velocity, quality, and reproducibility of your research.

Seqera Pipelines: Guiding Your Research Journey

In the early days of Nextflow, the “awesome-nextflow” GitHub repository was the go-to place to find pipelines. People would list their open-source workflows so that others could find one to match their data. Over time, the Nextflow community grew, and this particular resource became unmanageable. Projects such as nf-core have emerged with collections of workflows, but there are very many other high-quality Nextflow pipelines beyond nf-core that can be difficult to find.

Seqera Pipelines is the modern replacement for the “awesome-nextflow” repo. We’ve put together a list of the best open-source workflows for you to search. We know from experience that finding high-quality pipelines is critical, so we’re using a tightly curated list of the very best workflows to begin with. Every pipeline comes with curated test data, so you can import into Seqera Platform and launch a test run in just a few clicks:

Once you’ve found an interesting pipeline, you can easily dive into the details. We show key information on the pipeline details page and provide a one-click experience to add pipelines to your launchpad within Seqera Platform. If you’re more at home in the terminal, you can use the launch box to grab commands for Nextflow, Seqera Platform CLI, and nf-core/tools.

We have big plans for Seqera Pipelines. By prioritizing actively maintained pipelines that adhere to industry standards, we minimize the risk of researchers encountering obsolete or malfunctioning pipelines. As we improve our accuracy, we will open up the catalog to include greater numbers of workflows.

Discovering a workflow is only the first step of a journey. In the future, we will extend Seqera Pipelines with additional features, such as the ability to create collections of your favorite pipelines and discuss their usage – both to get help and to help others in the community. Seqera Pipelines is already the best place to find your next workflow, and it’s only going to get better.

Seqera Containers: The Magic of Reproducibility

Containers have transformed the research landscape, providing portable environments that encapsulate software, dependencies, and libraries – eliminating compatibility issues across various computing environments. Nextflow was a very early adopter of Docker and has provided first-class support for software containers for nearly a decade.

While using containers isn’t entirely without friction. Pipeline developers need to write Dockerfile scripts for each step in their workflow. Projects such as BioContainers have greatly simplified this process with pre-built images for Bioconda tools but are somewhat limited, especially when multiple tools are needed in a single container. We set out to improve this experience with Wave: our open-source on-demand container provisioning service. Wave allows Nextflow developers to simply reference a set of conda packages or a bundled Dockerfile. When the pipeline runs, the container is built on the fly and can be targeted for the specific local environment that the workflow is running in.

With Seqera Containers, we’re taking the experience of Wave one step further. Instead of browsing available images as you would with a traditional container registry, just type in the names of the tools you want to use. Clicking “Get container” returns a container URI instantly, which you can use for anything - Nextflow pipeline or not. The key difference with Seqera Containers is that the image is also stored in an image cache, with infrastructure provided by our friends at AWS. Subsequent requests for the same package set will return the same image, ensuring reproducibility across runs. The cache has no expiry date, so those images will still be there if you need to rerun your analysis in the future.

Not only can you request any combination of packages, but you can also select architecture and image format. Builds with linux/arm64 architecture promise to open up analysis to new, more efficient compute platforms. Choosing Singularity leads to a native Singularity / Apptainer build with an OCI-compliant architecture and even a URL to download the .sif file directly.

Clicking “View build details” for the container shows the full information of the Dockerfile, conda environment file, and build settings, as well as the complete build logs. Every container includes results from a security scan using Trivy attached.

While the web interface is the easiest way to get started with Seqera Containers, it doesn’t end there. The same functionality extends to Nextflow and the Wave CLI. Just tell Wave to “freeze” with a set of conda packages, and the resulting image will be cached in the public Seqera Containers registry.

Seqera Containers is a free service provided by Seqera and AWS. It does not require authentication of any kind to use, and is configured with very high rate limits so that nothing stops your pipeline from pulling 50 images all at once! We can’t wait to see how the entire bioinformatics community uses it, both Nextflow users and beyond.

What lies ahead

Pipelines and Containers represent just the beginning of Seqera’s vision to be the home of open science. We think that these two resources can have a real impact on researchers around the globe, and we’re excited to continue working with them to extend their functionality. We’re committed to collaborating with the community to focus on the features that you need, so do let us know what you think and what you want next!