This post has been written by our valued community members.
During my time at the University of Alabama at Birmingham (UAB), I have actively embraced workflow management systems since 2017. In 2021, my team at the UAB Biological Data Science Core (U-BDS) fully transitioned to using Nextflow and nf-core pipelines as our standard for all analytical processing which can be automated prior to data interpretation and visualization. The decision was straightforward: nf-core provided a strong community resource and incorporated many of the best practices I had already been implementing at U-BDS. This shift allowed us to streamline operations by eliminating the need to maintain multiple overlapping secondary analysis pipelines and instead focus our efforts on contributing directly to open-source resources and developing novel pipelines. To date, we not only implement nf-core and Nextflow pipelines routinely, we have also created UAB’s nf-core institutional profile and have also successfully released nf-core/scnanoseq, accompanied by a peer-reviewed publication which discusses the workflow implementation and validation of its outputs.
Despite these advances within U-BDS, I recognized that many in the broader UAB community were still unfamiliar with Nextflow, nf-core, or key concepts such as resource optimization that are critical for efficient use of these computational resources. While the U-BDS core had previously offered analytical workshops - such as bulk RNA-seq training using the nf-core/rnaseq pipeline and its outputs for downstream analysis - there had not yet been a dedicated training opportunity focused exclusively on Nextflow and nf-core. To address this gap, a member of my team, Austyn Trull, and I offered a new workshop aimed at providing researchers from diverse backgrounds with practical knowledge to effectively implement nf-core pipelines in their own work. With 50 participants across UAB trainees, staff and faculty, we had a very successful event.
Workshop Structure and Topics
The workshop was designed as a 4-hour, demonstration-based session covering the following:
- Overview of Nextflow and nf-core
- nf-core/rnaseq pipeline
- Overview of pipeline scope
- nf-core at UAB with the Cheaha profile
- Executing the pipeline
- Interpreting the outputs
- Reviewing Nextflow’s working directories and logs
- Seqera AI
All workshop materials were made available online, enabling participants to reproduce the analyses at their own pace. We also encourage others to use and adapt these materials as needed, with the request that proper citation be provided.
Introduction to Nextflow and nf-core
We began by introducing the core concepts of Nextflow and nf-core: what they are, what they represent, and why they are well suited for modern bioinformatics and computational biology. We highlighted the strengths of nf-core pipelines, emphasizing their reproducibility, structured design, and community-driven curation. Importantly, participants were introduced to nf-core’s broader community initiatives, including their active presence on Slack, social media (LinkedIn, Twitter, Bluesky), training events, bytesize talks and hackathons.
Demonstration: nf-core/rnaseq
For the main demonstration, we showcased the nf-core/rnaseq workflow. We provided:
- An overview of the pipeline’s key steps and how they relate to bulk RNA-seq data.
- A brief history of the pipeline’s development and community support.
- An emphasis on its maturity within nf-core, noting that while this workflow is well matured, that many principles demonstrated here apply to other nf-core workflows.
In addition, we provided a guided overview of the pipeline’s outputs including:
- Review of key quality-control metrics compiled by the MultiQC report
- Review of the Nextflow report to evaluate computational resource usage
- Brief overview of essential Nextflow generated files that can assist with troubleshooting.
Introduction to Seqera AI
Finally, we introduced Seqera AI to the UAB community by briefly discussing access to it via the web platform or the Nextflow VS Code extension. We demonstrated how Seqera AI can support users in tasks such as:
1. Writing a custom configuration file.
2. Navigating working directories (and why this is important).
3. Troubleshooting common errors.
We also emphasized that while Seqera AI is a valuable tool, it is not a substitute for foundational knowledge of Nextflow and the workflows themselves. Users will get the most benefit when combining Seqera AI with an understanding of the underlying pipeline.
Reflections and Feedback
The workshop received very positive feedback from participants, who appreciated both the practical demonstrations and the discussions on integrating AI-assisted tools into bioinformatics workflows. One participant shared that the session not only deepened their understanding of RNA-seq analysis but also inspired them to apply AI tools to debug and improve their own analysis. Another attendee highlighted that this was the first workshop at UAB focused specifically on workflow management systems - an initiative that opens new opportunities for the university to showcase and build upon its existing expertise in computational workflows. Among the workshop attendees, the following are direct testimonials:
“The Nextflow workshop organized by Dr. Lara Ianov was exceptionally informative and engaging. It provided a comprehensive overview of the framework, while also diving into the intricate nuances of integrating Nextflow into our local compute cluster environment, Cheaha. The workshop not only enhanced our technical understanding of the framework but also empowered us to make more confident and effective decisions in deploying scalable and reproducible genomic analytics pipelines within Cheaha."
Vinodh Srinivasasainagendra, Information Systems Manager II - Departments of Biostatistics
"The U-BDS workshop was a great introduction to Nextflow and the nf-core RNA-seq pipeline. After attending the workshop with a few of my students, I feel confident in my lab moving forward with performing more in-house analysis of our RNA sequencing experiments."
Dr. Andrew Arrant, Associate Professor - Department of Neurology
“The workshop was a great overview and technical introduction to the Nextflow tool, and really made clear the amount of work that the nf-core community has put into making re-usable tools that can accelerate and standardize NGS based analyses. It was very useful for understanding what it would take to transition from some of our current, bespoke, Snakemake pipelines to more open sourced and community based Nextflow implementations. It was also nice to get a quick overview of the Sequera AI assistant.”
Curtis Hendrickson, Scientist III - Department of Microbiology
“The workshop was extremely helpful, and I was impressed by the user-friendly and well-organized nf-core RNA-seq pipeline, its flexibility to adjust parameters, and its seamless use in an HPC environment - I look forward to its expansion into areas like scRNA-seq and spatial transcriptomics.”
Hyunmin Koo, Bioinformatics Scientist - Institutional Research Core Program
From my perspective, this workshop reinforced the value of demonstration-based learning and the importance of connecting theoretical workflow principles with real-world application. For an audience with diverse backgrounds across different scientific domains, live demonstrations are particularly impactful. They bridge the gap between abstract computational concepts and the practical steps needed to analyze and interpret biological data.
Looking ahead, one improvement I would like to implement in future sessions (time permitting) is the inclusion of additional nf-core workflows, such as nf-core/nanoseq. Since it also deals with bulk RNA-seq data, this workflow would provide an excellent opportunity to demonstrate how key workflow concepts are transferable across pipelines while highlighting unique aspects of each workflow across different types of data modalities. This would further strengthen participants’ understanding of nf-core’s design principles and enhance their confidence in adapting workflows to their own research needs.
Nextflow Ambassador Program
Thanks to the Nextflow Ambassador Program, our workshop participants were able to enjoy a half-day of learning without an empty stomach - as a Nextflow Ambassador, the program generously covered both breakfast and lunch. This was my first experience receiving support from the program for a community event, and it made a meaningful difference. In today’s climate of financial constraints across academic institutions, this kind of support is especially valuable and greatly appreciated. I would like to extend a special thanks to Marcel Ribeiro-Dantas (Seqera) and Kate Daughtry (UAB) for their timely assistance in ensuring all arrangements were handled smoothly.