The Seqera Blog

Seqera Co-Scientist Brings GPU Acceleration to Nextflow Pipelines with NVIDIA BioNeMo Agent Toolkit
Seqera

Seqera Co-Scientist Brings GPU Acceleration to Nextflow Pipelines with NVIDIA BioNeMo Agent Toolkit

Co-Scientist is built to meet scientists wherever they work, including helping teams build, debug, optimize, and modernize their Nextflow pipelines with AI that understands their environment. Today, with the launch of the NVIDIA BioNeMo Agent Toolkit, we’re taking the next step. Teams can now more easily bring the power of accelerated computing and AI agents to their Nextflow pipelines.

Drew DiPalmaDrew DiPalma
Jun 23, 2026

Community

SeqeraCommunity

rewrites.bio: Principles for AI-assisted Modernization of Scientific Software

A wave of AI-driven tool rewrites is coming to bioinformatics. We've published a set of best-practices principles to try to help people to approach rewrites in the right way.

Phil EwelsPhil Ewels
Apr 02, 2026
NextflowCommunity

From Complete Beginner to nf-core Contributor

As part of my training in the scientist training programme, I undertook a Master’s project to develop, validate, and implement a long-read bioinformatics pipeline for rare disease diagnostics using Nextflow.

Nour MahfelNour Mahfel
Jan 20, 2026
CommunityNextflow

Paving the Way for the Next Generation of Nextflow Ambassadors in Africa

As Nextflow Ambassadors, embarked on an inspiring journey to empower the next Tunisian generation of bioinformaticians and more across Africa - through the power of Nextflow.

Firas ZemzemFiras Zemzem
Dec 15, 2025
CommunitySeqera

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

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
Oct 14, 2025
NextflowCommunity

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

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
Sep 22, 2025
NextflowCommunity

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

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
Jul 01, 2025
NextflowCommunity

VIRUS-MVP: A scalable and flexible pathogen surveillance workflow powered by Nextflow and nf-core

VIRUS-MVP leverages Nextflow and nf-core to provide a modular, automated, and scalable framework for genomic surveillance of priority viruses. Designed initially for SARS-CoV-2, the workflow was later adapted or is in development for other priority viruses, including Mpox, respiratory syncytial virus (RSV), and influenza.

Zohaib AnwarZohaib Anwar
May 09, 2025
NextflowCommunity

Automating SRA data access and processing with Nextflow

Handling large-scale genomic data efficiently is one of the most pressing challenges in bioinformatics. My work on pediatric gliomas requires processing vast amounts of RNA-seq data from publicly available repositories like the Sequence Read Archive (SRA). Traditional methods of handling these datasets involved labor-intensive manual downloads and data validation processes. This approach was time-consuming, error-prone, and lacked reproducibility. To address these issues, I developed biopy_sra.nf, a Nextflow pipeline designed to automate the process of accessing, downloading, and preprocessing RNA-seq data from SRA.

Gisela PattaroneGisela Pattarone
Mar 19, 2025
NextflowCommunity

From Hackathon to policy: Why COP16 Policy Matters for Nextflow Users

Do you process genetic sequences in your Nextflow workflows? Are you part of a research community or industry that depends on digital sequence information (DSI)? If so, you’ll want to know about the key outcomes from COP16 on Biological Diversity, held in Cali, Colombia, last fall.

Solenne Correard
Camila Mazzoni
Solenne Correard &  Camila Mazzoni
Feb 25, 2025
NextflowCommunity

Join us in welcoming the first cohort of 2025 Nextflow Ambassadors

It's time to welcome the new ambassadors who joined the Nextflow Ambassador Program for the 2025.1 semester.

Marcel Ribeiro-DantasMarcel Ribeiro-Dantas
Jan 21, 2025
CommunityNextflow

Building an nf-core style modules library for your organization

If you would like to bring nf-core’s approach to enabling code within your own organization, you can!

Ken BrewerKen Brewer
Jan 02, 2025
NextflowCommunity

How Nextflow builds key software development skills for bioinformaticians

I first used Nextflow at 19 years old, a year out of school during the first year of my apprenticeship. Over the next 5 years, I acquired a diverse set of essential skills that enabled me to explore a wide range of career opportunities by building Nextflow pipelines.

Simon MurraySimon Murray
Dec 02, 2024
NextflowCommunity

Nextflow and Seqera containers: a lifesaver for bioinformatics work on HPC environments

In bioinformatics and data science, handling large datasets and dependencies is crucial. Nextflow, a powerful domain-specific language, enables efficient, reproducible workflows across local and cloud platforms. In this post, I share how Nextflow and Seqera Containers have revolutionized my work in the Oncology Data Science group at Novartis, Cambridge, MA, allowing us to optimize complex computational workflows seamlessly.

Charalampos Lazaris, Ph.D.Charalampos Lazaris, Ph.D.
Nov 13, 2024
NextflowCommunity

Nextflow workflow: from HPC to Cloud

Bioinformaticians often run their Nextflow workflows on internal HPC clusters, typically using job schedulers like Slurm to manage tasks. However, as the need for scalability and flexibility grows, many are making the shift to public cloud platforms. In this post, we'll highlight key details from a recent real-world example to demonstrate details about this process.

Lynn Langit
David Haley
Lynn Langit & David Haley
Oct 23, 2024
NextflowCommunity

Daisy-chaining workflows: the nf-cascade concept

Nextflow workflows are widely used across various fields, performing tasks ranging from data retrieval and cleaning to processing and downstream analyses. Generally, workflows which feed into other workflows are run independently. They are also often not written in a way they can be included directly as subworkflows into another workflow, making it challenging to connect them seamlessly. nf-cascade is a proof-of-concept pipeline that demonstrates how multiple existing workflows can be integrated into a single workflow. Specifically, the proof-of-concept connects the nf-core pipelines: nf-core/fetchngs, nf-core/taxprofiler, nf-core/mag, and nf-core/funcscan. The code can be generalised further to run and connect any existing workflow, without any modifications necessary to the workflows you want to run.

Mahesh Binzer-PanchalMahesh Binzer-Panchal
Oct 09, 2024
NextflowCommunity

My Journey with Nextflow: From Exploration to Automation

I approach bioinformatics workflows in a whole different way now that I’ve used Nextflow. It has evolved into a vital tool in my toolbox, capable of handling massive genomic datasets and guaranteeing repeatability and scalability. Thanks to Nextflow, I can automate and streamline tasks that used to take days or even weeks, whether it’s merging disparate software applications or simplifying intricate pipelines. To go beyond the constraints of conventional scripting (bash, perl, Python, R) for genomic data analysis was the driving force for my decision to work with Nextflow. Since then, it’s opened up new possibilities, leading me to collaborations, innovation, and now this exciting new role as an Ambassador! I am Pritam Kumar Panda, a bioinformatician working at the German Cancer Research Center DKFZ, Heidelberg, Germany.

Pritam Kumar PandaPritam Kumar Panda
Sep 25, 2024
NextflowCommunity

Addressing Bioinformatics Core Challenges with Nextflow and nf-core

I was honored to be invited to the ISMB 2024 congress to speak at the session organised by the COSI (Community of Special Interest) of Bioinformatics Cores. This session brought together bioinformatics professionals from around the world who manage bioinformatics facilities in different institutions to share experiences, discuss challenges, and explore solutions for managing and analyzing large-scale biological data. In this session, I had the opportunity to introduce Nextflow, and discuss how its adoption can help bioinformatics cores to address some of the most common challenges they face.

Francesco LescaiFrancesco Lescai
Sep 11, 2024
NextflowCommunity

Moving toward better support through the Community forum

As the Nextflow community continues to grow, fostering a space where users can easily find help and share knowledge is more important than ever. In this post, we’ll explore our ongoing efforts to enhance the community forum, transitioning from Slack as the primary platform for peer-to-peer support.

Geraldine Van der AuweraGeraldine Van der Auwera
Aug 28, 2024
NextflowCommunity

How I became a Nextflow Ambassador!

As a PhD student in bioinformatics, I aimed to build robust pipelines to analyze diverse datasets throughout my research. Initially, mastering Bash scripting was a time-consuming challenge, but this journey ultimately led me to become a Nextflow Ambassador, engaging actively with the expert Nextflow community.

Firas ZemzemFiras Zemzem
Jul 24, 2024
NextflowCommunity

The State of the Workflow 2024: Community Survey Results

State of the Workflow 2024 Community Survey Results: Insights from 600+ Nextflow users about the state of workflow management for scientific data analysis

Evan FlodenEvan Floden
Jul 17, 2024
NextflowCommunity

Reflecting on a six-month collaboration: insights from a Nextflow Ambassador

As a Nextflow Ambassador and a PhD student working in bioinformatics, I’ve always believed in the power of collaboration. Over the past six months, I’ve had the privilege of working with another PhD student specializing in metagenomics environmental science. This collaboration began through a simple email after the other researcher discovered my contact information on the ambassadors’ list page.

Cristina Tuñi i DomínguezCristina Tuñi i Domínguez
Jun 19, 2024
NextflowCommunity

Fostering Bioinformatics Growth in Türkiye

After diving into the Nextflow community, I’ve seen how it benefits bioinformatics in places like South Africa, Brazil, and France. I’m confident it can do the same for Türkiye by fostering collaboration and speeding up research. Since I became a Nextflow Ambassador, I am happy and excited because I can contribute to this development!

Kübra NarcıKübra Narcı
Jun 12, 2024
NextflowCommunity

Open call for new Nextflow Ambassadors closes June 14

Nextflow Ambassadors are passionate individuals within the Nextflow community who play a more active role in fostering collaboration, knowledge sharing, and engagement. We launched this program at the Nextflow Summit in Barcelona last year, and it’s been a great experience so far, so we’ve been recruiting more volunteers to expand the program.

Marcel Ribeiro-DantasMarcel Ribeiro-Dantas
May 17, 2024
NextflowCommunity

Nextflow Training: Bridging Online Learning with In-Person Connections

Nextflow and nf-core provide frequent community training events to new users, which offer an opportunity to get started using and understanding Nextflow, Groovy and nf-core. These events are live-streamed and are available for on-demand viewing on YouTube, but what if you could join friends in person and watch it live?

Florian Wuennemann
Kübra Narcı
Florian Wuennemann & Kübra Narcı
May 08, 2024
NextflowCommunity

nf-schema: the new and improved nf-validation

Check out Nextflow's newest plugin, nf-schema! It's an enhanced version of nf-validation, utilizing JSON schemas to validate parameters and sample sheets. Unlike its predecessor, it supports the latest JSON schema draft and can convert pipeline-generated files. But what's the story behind its development?

Nicolas VannieuwkerkeNicolas Vannieuwkerke
May 01, 2024
NextflowCommunity

Empowering bioinformatics: mentoring across continents with Nextflow

In my journey with the nf-core Mentorship Program, I’ve mentored individuals from Malawi, Chile, and Brazil, guiding them through Nextflow and nf-core. Despite the distances, my mentees successfully adapted their workflows, contributing to the open-source community. Witnessing the transformative impact of mentorship firsthand, I’m encouraged to continue participating in future mentorship efforts and urge others to join this rewarding experience. But how did it all start?

Robert PetitRobert Petit
Apr 25, 2024
NextflowCommunity

Application of Nextflow and nf-core to ancient environmental eDNA

Ancient environmental DNA (eDNA) is currently a hot topic in archaeological, ecological, and metagenomic research fields. Recent eDNA studies have shown that authentic ‘ancient’ DNA can be recovered from soil and sediments even as far back as 2 million years ago.

James Fellows YatesJames Fellows Yates
Apr 17, 2024
NextflowCommunity

One-year reflections on Nextflow Mentorship

From December 2022 to March 2023, I was part of the second cohort of the Nextflow and nf-core mentorship program, which spanned four months and attracted participants globally. I could not have anticipated the extent to which my participation in this program and the associated learning experiences would positively change my professional growth.

Anabella TrigilaAnabella Trigila
Apr 10, 2024
NextflowCommunity

Leveraging nf-test for enhanced quality control in nf-core

Reproducibility is an important attribute of all good science. This is especially true in the realm of bioinformatics, where software is hopefully being updated, and pipelines are ideally being maintained. Improvements and maintenance are great, but they also bring about an important question: Do bioinformatics tools and pipelines continue to run successfully and produce consistent results despite these changes? Fortunately for us, there is an existing approach to ensure software reproducibility: testing.

Sateesh Peri
Carson Miller
Sateesh Peri & Carson Miller
Apr 03, 2024
NextflowCommunity

Nextflow workshop at the 20th KOGO Winter Symposium

Through a partnership between AWS Asia Pacific and Japan, and Seqera, Nextflow touched ground in South Korea for the first time with a training session at the Korea Genome Organization (KOGO) Winter Symposium. The objective was to introduce participants to Nextflow, empowering them to craft their own pipelines. Recognizing the interest among bioinformaticians, MinSung Cho from AWS Korea’s Healthcare & Research Team decided to sponsor this 90-minute workshop session. This initiative covered my travel expenses and accommodations.

Yuk Kei WanYuk Kei Wan
Mar 14, 2024
NextflowCommunity

Introducing the Nextflow Ambassador Program

We are excited to announce the launch of the Nextflow Ambassador Program, a worldwide initiative designed to foster collaboration, knowledge sharing, and community growth. It is intended to recognize and support the efforts of our community leaders and marks another step forward in our mission to advance scientific research and empower researchers

Marcel Ribeiro-DantasMarcel Ribeiro-Dantas
Oct 18, 2023
NextflowCommunity

Introducing community.seqera.io

We are very excited to introduce the Seqera community forum - the new home of the Nextflow community!

Oct 18, 2023
NextflowPeopleCommunity

Geraldine Van der Auwera joins Seqera

We're excited to welcome Geraldine to Seqera as Lead Developer Advocate to help the Nextflow community in the USA grow and thrive!

Geraldine Van der AuweraGeraldine Van der Auwera
Oct 11, 2023
NextflowCommunity

Celebrating our largest international training event and hackathon to date

In mid-March, we conducted our bi-annual Nextflow and nf-core training and hackathon in what was unquestionably our best-attended community events to date. This year we had an impressive 1,345 participants attend the training from 76 countries. Attendees came from far and wide — from Algeria to Andorra to Zambia to Zimbabwe!

Apr 25, 2023
NextflowCommunityAnnouncement

The State of the Workflow 2023: Community Survey Results

In March, we ran our annual State of the Workflow Community survey to get a sense of activities and preferences in the Nextflow user community.

Evan FlodenEvan Floden
Apr 25, 2023
NextflowCommunity

Nextflow and nf-core Mentorship, Round 2

The global Nextflow and nf-core community is thriving with strong engagement in several countries. As we continue to expand and grow, we remain committed to prioritizing inclusivity and actively reaching groups with low representation.

Chris HakkaartChris Hakkaart
Apr 17, 2023
NextflowCommunityAnnouncement

The State of the Workflow 2023: The Nextflow and nf-core community survey

Get an opportunity to win an Apple Macbook Air M2 or one of ten sustainability-certified Seqera merchandise packs

Evan FlodenEvan Floden
Mar 01, 2023
NextflowCommunity

Nextflow and nf-core mentorship, Round 1

Our recent The State of the Workflow 2022: Community Survey Results showed that Nextflow and nf-core have a strong global community with a high level of engagement in several countries. As the community continues to grow, we aim to prioritize inclusivity for everyone through active outreach to groups with low representation.

Chris HakkaartChris Hakkaart
Sep 18, 2022
CommunityNextflow

Nextflowomics: Untangling Biology with Data Analysis Pipelines

An overview of the omics disciplines and the role of Nextflow and cloud computing in advancing research

Harshil PatelHarshil Patel
Jul 18, 2022
NextflowCommunityAnnouncement

The State of the Workflow 2022: Community Survey Results

The State of the Workflow 2022: The Nextflow and nf-core Community. The results from our Nextflow user survey, covering where and how people use Nextflow and nf-core.

Gord SissonsGord Sissons
May 23, 2022
NextflowMultiQCPeopleCommunity

Phil Ewels joins Seqera

Phil Ewels outlines his journey, from his beginnings in the Babraham Institute, his time at SciLifeLab, to working full-time with Nextflow.

Phil EwelsPhil Ewels
Mar 22, 2022
Community

Nextflow’s community is moving to Slack!

The Nextflow community channel on Gitter has grown substantially over the last few years and today has more than 1,300 members.

Paolo Di TommasoPaolo Di Tommaso
Feb 22, 2022
NextflowCommunityAnnouncement

State of the Workflow 2022: The Nextflow and nf-core community survey

Win an Apple Macbook Air M1 along with one of ten Seqera merch packs

Evan FlodenEvan Floden
Feb 08, 2022
Community

Announcing the Nextflow Tower CLI

Blog post covering the new Tower command-line interface. Launch pipelines, manage cloud resources, and administer Tower with the new CLI.

Evan FlodenEvan Floden
Dec 14, 2021
NextflowPeopleCommunity

Introducing Harshil Patel, Head of Scientific Development

Dr. Harshil Patel's journey to leading pipeline development at the home of Nextflow and nurturing the relationship between nf-core and Seqera.

Harshil PatelHarshil Patel
Nov 22, 2021
Community

Introducing the Tower Cloud Community Workspace

With the Community Showcase, Tower Cloud provides ready-to-go analysis environments & gold-standard pipelines

Evan FlodenEvan Floden
Oct 22, 2021
Community

Personalized Immunotherapy – Machine Learning meets Next Generation Sequencing

Personalized Immunotherapy – Machine Learning meets Next Generation Sequencing with the amazing work of Gritstone bio

Robert LalondeRobert Lalonde
Aug 02, 2021
NextflowAnnouncementCommunity

nf-core June 2021 Updates - The latest news from the nf-core team

A guest post on the June 2021 updates, including the march towards Nextflow DSL2, with Phil Ewels from the nf-core community.

Phil EwelsPhil Ewels
Jul 02, 2021
PartnersCommunity

RNA Society Hosts APAeval Challenge on Nextflow Tower

An overview of APAeval, the collaborative effort to advance computation methods within the RNA Community

Evan FlodenEvan Floden
Jun 03, 2021
NextflowCommunityAnnouncement

The State of Nextflow 2021

The State of Nextflow 2021 - the results from our Nextflow user survey, covering where and how people use Nextflow, their industry, and their teams.

Evan FlodenEvan Floden
Mar 10, 2021
Community

Tower API & Docs release

A year after Tower's release, Seqera presents two milestones: Tower API & Docs, which bring massively scalable data analysis pipelines to everybody

Evan FlodenEvan Floden
Nov 05, 2020
AnnouncementCommunity

Sharing is Caring

Seqera celebrates the first birthday of the Tower project - our mission to deliver the most seamless experience for data analysis pipelines

Paolo Di TommasoPaolo Di Tommaso
Oct 08, 2020
AnnouncementCommunityPeopleNextflow

Day one

Day one! We are thrilled to announce the launch of Seqera, founded by Paolo Di Tommaso and Evan Floden.

Evan FlodenEvan Floden
Jun 16, 2019