Community | Seqera

Posts tagged with "Community"

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 Anwar

Automating SRA data access and processing with Nextflow

Mar 19, 2025

NextflowCommunity

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 Pattarone

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

Feb 25, 2025

NextflowCommunity

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

Join us in welcoming the first cohort of 2025 Nextflow Ambassadors

Jan 21, 2025

NextflowCommunity

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

Marcel Ribeiro-Dantas

Building an nf-core style modules library for your organization

Jan 02, 2025

CommunityNextflow

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

Ken Brewer

How Nextflow builds key software development skills for bioinformaticians

Dec 02, 2024

NextflowCommunity

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 Murray

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

Nov 13, 2024

NextflowCommunity

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.

Nextflow workflow: from HPC to Cloud

Oct 23, 2024

NextflowCommunity

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

Daisy-chaining workflows: the nf-cascade concept

Oct 09, 2024

NextflowCommunity

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

My Journey with Nextflow: From Exploration to Automation

Sep 25, 2024

NextflowCommunity

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

Addressing Bioinformatics Core Challenges with Nextflow and nf-core

Sep 11, 2024

NextflowCommunity

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

Moving toward better support through the Community forum

Aug 28, 2024

NextflowCommunity

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

How I became a Nextflow Ambassador!

Jul 24, 2024

NextflowCommunity

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

The State of the Workflow 2024: Community Survey Results

Jul 17, 2024

NextflowCommunity

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

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

Jun 19, 2024

NextflowCommunity

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

Fostering Bioinformatics Growth in Türkiye

Jun 12, 2024

NextflowCommunity

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

Open call for new Nextflow Ambassadors closes June 14

May 17, 2024

NextflowCommunity

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 Training: Bridging Online Learning with In-Person Connections

May 08, 2024

NextflowCommunity

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

nf-schema: the new and improved nf-validation

May 01, 2024

NextflowCommunity

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

Empowering bioinformatics: mentoring across continents with Nextflow

Apr 25, 2024

NextflowCommunity

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

Application of Nextflow and nf-core to ancient environmental eDNA

Apr 17, 2024

NextflowCommunity

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

One-year reflections on Nextflow Mentorship

Apr 10, 2024

NextflowCommunity

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

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

Apr 03, 2024

NextflowCommunity

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

Nextflow workshop at the 20th KOGO Winter Symposium

Mar 14, 2024

NextflowCommunity

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

Introducing the Nextflow Ambassador Program

Oct 18, 2023

NextflowCommunity

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

Introducing community.seqera.io

Oct 18, 2023

NextflowCommunity

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

Geraldine Van der Auwera joins Seqera

Oct 11, 2023

NextflowPeopleCommunity

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

Celebrating our largest international training event and hackathon to date

Apr 25, 2023

NextflowCommunity

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 State of the Workflow 2023: Community Survey Results

Apr 25, 2023

NextflowCommunityAnnouncement

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 Floden

Nextflow and nf-core Mentorship, Round 2

Apr 17, 2023

NextflowCommunity

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

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

Mar 01, 2023

NextflowCommunityAnnouncement

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

Evan Floden

Nextflow and nf-core mentorship, Round 1

Sep 18, 2022

NextflowCommunity

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

Nextflowomics: Untangling Biology with Data Analysis Pipelines

Jul 18, 2022

CommunityNextflow

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: Community Survey Results

May 23, 2022

NextflowCommunityAnnouncement

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.