Nextflow 25.10 and the New Plugin Registry: Major Updates for the Bioinformatics Community

Oct 24, 2025
Nextflow

Today, we're excited to announce key updates in Nextflow 25.10, including static types, workflow inputs and outputs, new commands (nextflow auth and nextflow launch), and S3 performance improvements. We've also launched the official Nextflow Plugin Registry to streamline plugin discovery and management across the community.

Ben Sherman
Phil Ewels
Paolo Di Tommaso
Ben Sherman, Phil Ewels & Paolo Di Tommaso

MultiQC Turns 10: Shaping the Gold Standard in Bioinformatics Reporting

Oct 24, 2025
MultiQC

Ten years ago, a simple idea emerged: what if we could visualize QC metrics in a single, interactive report? That became MultiQC, and today we're celebrating a decade of transforming bioinformatics worldwide.

Phil EwelsPhil Ewels

What’s New at Seqera: GxP-Aligned Bioinformatics, Expanded Data Connections, AI Integrations, and More

Oct 23, 2025
Seqera Platform

I began today's Nextflow Summit talking about our vision to make scientists' lives simpler, one pipeline at a time. The same platform, but better suited to bioinformatics in 2025. Every product update we’ve announced today builds on this foundation, moving us through the complete journey from scientific infrastructure, through innovation and velocity. From GxP-aligned pipeline versioning and in-platform data exploration on HPC, to AI in Platform and our new MCP Server, here’s the latest Seqera updates you won’t want to miss.

Evan FlodenEvan Floden

Efficient S3 Transfers in Nextflow: Moving to AWS SDK v2

Oct 23, 2025
Nextflow

The upcoming 25.10 release of Nextflow uses the AWS Java SDK v2, which brings a significant performance boost to pipelines running on Amazon S3. In this blog post, we will show how this new version of Nextflow improves S3 performance, both at the level of basic S3 operations and end-to-end workflow runs.

Jorge Ejarque
Ben Sherman
Jorge Ejarque & Ben Sherman

Enabling Single-Cell Benchmarks at Scale: The OpenProblems.bio, Viash, and Seqera Partnership

Oct 14, 2025
Seqera PlatformCommunity

Single-cell analysis sits at the intersection of machine learning and biology. Advances in microfluidic technology have transformed data collection, creating large, tabular datasets well suited to machine-learning (ML) methods. OpenProblems.bio formalizes evaluating approaches into living, community‑run benchmarks (curated tasks, datasets, methods, and metrics) and then executes them as robust pipelines.

Evan Floden
Robrecht Cannoodt
Evan Floden & Robrecht Cannoodt

Introducing the Seqera MCP Server: Bringing Seqera to Your Preferred AI Agent

Oct 09, 2025
Seqera Platform

The AI revolution is reshaping how we interact with computational infrastructure. We recently announced the Seqera AI Integration in Platform, our purpose-built bioinformatics AI that can directly execute, debug, and launch workflows within Seqera Platform. Today, we're taking the next decisive step forward by opening Seqera to the entire AI ecosystem through our new Seqera MCP server. Fully integrated with Seqera single sign on (SSO), you can make your preferred AI tool (e.g. Claude AI, VS Code Copilot, Cursor) your new control center for Seqera Platform.

Paolo Di TommasoPaolo Di Tommaso

Achieve Granular Cloud Resource Tracking with Dynamic Resource Labels

Oct 07, 2025
Seqera Platform

Today, we are excited to announce dynamic resource labels — a new Seqera Platform feature that solves the per-workflow cost tracking challenge by automatically injecting unique workflow and session identifiers into every cloud job. This removes the necessity for manual configuration, whether your workflows run in AWS, Azure, or Google Cloud.

Anton Tsyganov-Bodounov
Llewellyn van der Berg
Anton Tsyganov-Bodounov & Llewellyn van der Berg

MAGFlow/BIgMAG: The Batman & Robin of the Metagenomics Field

Sep 22, 2025
NextflowCommunity

In the metagenomics field, there are at least 33 bioinformatics pipelines aimed at recovering MAGs (please check 2Pipe), and you may wonder: do I obtain the same results with different pipelines? How do they compare in terms of genome quality and completeness? Do my bins (draft MAGs) match the Minimum Information about a MAG (MIMAG criteria)? Is the taxonomic assignment of the bin shared across pipeline outputs? For instance, let’s say that you’ve run three different binning tools and a handful of quality-measuring software, how do you keep track of all those results without drowning in TSV files?

Jeferyd Yepes GarcíaJeferyd Yepes García

6 Reasons Why Bioinformatics is Hard and How Seqera Helps

Sep 18, 2025
Seqera Platform

As science accelerated, teams needed more than just workflow tools, they needed better data integration, scalability, and collaboration. Scientific progress was getting stuck because the technology was too complex. That’s why we created Nextflow and Seqera. In the blog post, we highlight six core problems that make bioinformatics harder than it should be and how Seqera, the Nextflow-first tech stack, addresses each one.

Esha JoshiEsha Joshi

Seqera AI in Platform: Develop, Debug, and Execute in One Unified Experience

Sep 16, 2025
Seqera Platform

Today, we're excited to announce that Seqera AI now has read and write access to Seqera Platform. This enables Seqera AI to directly interact with Seqera Platform primitives to debug pipelines, modify parameters, and launch runs, all without switching context between different tools and interfaces.

Sasha DagayevSasha Dagayev

What’s New: Seqera Platform Enterprise Release 25.2

Sep 04, 2025
Seqera Platform

Seqera Platform Enterprise 25.2 delivers significant enhancements across security, observability, and flexibility to accelerate your workflow orchestration capabilities. Key updates in this release include redesigned user interfaces, expanded cloud support, and powerful new development tools.

Drew DiPalmaDrew DiPalma

Nebulaworks and Nextflow: Scaling Machine-Learning in Pharma

Aug 27, 2025
Nextflow

Nextflow, combined with Nebulaworks’ implementation expertise, delivers scalable, reproducible ML pipelines that integrate MLflow experiment tracking with portable workflow orchestration, unifying pharmaceutical teams and accelerating drug discovery.

Anthony Ramirez
Rob Syme
Anthony Ramirez & Rob Syme

Optimizing High-Throughput Bioinformatics with Fusion

Aug 19, 2025
Seqera Platform

Fusion is the cloud-native file system designed and optimized for Nextflow pipelines that removes these barriers. It simplifies infrastructure, enhances performance, and cuts costs, making it easier for bioinformaticians to develop, maintain, and scale pipeline code.

Paolo Di TommasoPaolo Di Tommaso

Scaling with Seqera: From Prototype to Enterprise-Grade Deployment

Aug 14, 2025
Seqera Platform

Modern scientific research doesn’t just scale up, it scales in every direction: across code, compute, teams, and projects. Today, success isn’t measured by how much data is processed, but by how rapidly teams can adapt, reproduce results, and scale efficiently. Seqera exists to enable this. In this blog, we explore how the Seqera ecosystem empowers R&D leaders to scale innovation, streamline operations, and deliver faster, more reproducible scientific outcomes.

Esha JoshiEsha Joshi

Accelerating Innovation: Inside the Genomics England Hackathon 2025

Aug 06, 2025
Seqera

Last month, Seqera hosted a hackathon with Genomics England, bringing together bioinformaticians and Nextflow experts to tackle real-world challenges and enhance workflow capabilities. Over 2 days, teams tackled several critical projects, from following nf-core best practices to converting legacy WDL variant calling pipelines to Nextflow. The goal was to accelerate development, build technical confidence, and embed best practices across Genomics England.

Rike Hanssen
Adam Talbot
Harshil Patel
Rike Hanssen, Adam Talbot & Harshil Patel

Teaching, Training, and Transforming: Building Capacity with Nextflow in Vermont

Jul 01, 2025
NextflowCommunity

In our work within a busy core facility as well as for an infectious diseases group at the University of Vermont, we have to collaborate with many investigators and students. I discovered Nextflow and started using it intensively last year and haven't looked back. Currently I use Nextflow and nf-core for most of my projects. Here I want to discuss how I have used it for collaborations.

Ramiro Barrantes ReynoldsRamiro Barrantes Reynolds