The Open Science Blog

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.

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

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-Panchal

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 Panda

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 Lescai

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 Auwera

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 Zemzem

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

Evan Floden

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 Domínguez

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 Narcı

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-Dantas

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

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 Vannieuwkerke

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 Petit

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 Yates

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 Trigila

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

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 Wan

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-Dantas

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

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 Auwera

I’m excited to announce that I’m joining Seqera as Lead Developer Advocate. My mission is to support the growth of the Nextflow user community, especially in the USA, which will involve running community events, conducting training sessions, managing communications and working globally with our partners across the field to ensure Nextflow users have what they need to be successful. I’ll be working remotely from Boston, in collaboration with Paolo, Phil and the rest of the Nextflow team.

Geraldine Van der Auwera

Read about our State of the Workflow Community survey to get a sense of activities and preferences in the Nextflow user community.

Evan Floden

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!

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 Hakkaart

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

Evan Floden

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 Hakkaart

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

Harshil Patel

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 Sissons

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

Phil Ewels

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

Evan Floden

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

Harshil Patel

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

Phil Ewels

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 Floden

State of Nextflow Survey 2021

Evan Floden

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

Evan Floden