Empowering Bioinformatics: Mentoring Across Continents with Nextflow

  • Robert Petit
  • 25 April 2024
  • Community Post

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?

I’m Robert Petit, a bioinformatician at the Wyoming Public Health Laboratory, in Wyoming, USA. If you don’t know where that is, haha that’s fine, I’m pretty sure half the people in the US don’t know either! Wyoming is the 10th largest US state (253,000 km2), but the least populated with only about 580,000 people. It’s home to some very beautiful mountains and national parks, large animals including bears, wolves and the fastest land animal in the northern hemisphere, the Pronghorn. But it’s rural, can get cold (-10 C) and the high wind speeds (somedays average 50 kmph, with gusts 100+ kmph) only make it feel colder during the winter (sometimes feeling like -60 C to -40 C). You might be wondering:

How did some random person from Wyoming get involved in the nf-core Mentorship Program, and end up being the only mentor to have participated in all three rounds?

I’ve been in the Nextflow world for over 7 years now (as of 2024), when I first converted a pipeline, Staphopia from Ruffus to Nextflow. Eventually, I would develop Bactopia, one of the leading and longest maintained (5 years now!) Nextflow pipelines for the analysis of Bacterial genomes. Through Bactopia, I’ve had the opportunity to help people all around the world get started using Nextflow and analyzing their own bacterial sequencing. It has also allowed me to make numerous contributions to nf-core, mostly through the nf-core/modules. So, when I heard about the opportunity to be a mentor in the nf-core’s Mentorship Program, I immediately applied.

Round 1! To be honest, I didn’t know what to expect from the program. Only that I would help a mentee with whatever they needed related to Nextflow and nf-core. Then at the first meeting, I learned I would be working with Phil Ashton the Lead Bioinformatcian at Malawi Liverpool Wellcome Trust, in Blantyre, Malawi, and immediately sent him a “Yo!”. Phil and I had run into each other in the past because when it comes to bacterial genomics, the field is very small! Phil’s goal was to get Nextflow pipelines running on their infrastructure in Malawi to help with their public health response. We would end up using Bactopia as the model. But this mentorship wasn’t just about “running Bactopia”, for Phil it was important we built a basic understanding of how things are working on the back-end with Nextflow. In the end, Phil was able to get Nextflow, and Bactopia running, using Singularity, but also gain a better understanding of Nextflow by writing his own Nextflow code.

Round 2! When Round 2 was announced, I didn’t hesitate to apply again as a mentor. This time, I would be paired up with Juan Ugalde, an Assistant Professor at Universidad Andres Bello in Santiago, Chile. I think Juan and I were both excited by this, as similar to Phil, Juan and I had run into each other (virtually) through MetaSub, a project to sequence samples taken from public transport systems across the globe. Like many during the COVID-19 pandemic, Juan was pulled into the response, during which he began looking into Nextflow for other viruses. In particular, hantavirus, a public health concern due to it being endemic in parts of Chile. Juan had developed a pipeline for hantavirus sequence analysis, and his goal was to convert it into Nextflow. Throughout this Juan got to learn about the nf-core community and Nextflow development, which he was successful at! As he was able to convert his pipeline into Nextflow and make it publicly available as hantaflow.

Round 3! Well Round 3 almost didn’t happen for me, but I’m glad it did happen! At the first meeting, I learned I would be paired with Ícaro Maia Santos de Castro, at the time a PhD candidate at the University of São Paulo, in São Paulo, Brazil. We quickly learned we were both fans of One Piece, as Ícaro’s GitHub picture was Luffy from One Piece, haha and my background included a poster from One Piece. With Ícaro, we were starting with the basics of Nextflow (e.g. the nf-core training materials) with the goal of writing a Nextflow pipeline for his meta-transcriptomics dissertation work. We set the goal to develop his Nextflow pipeline, before an overseas move he had a few months away. He brought so many questions, his motivation never waned, and once he was asking questions about Channel Operators, I knew he was ready to write his pipeline. While writing his pipeline he learned about the nf-core/tools and also got to submit a new recipe to Bioconda, and modules to nf-core. By the end of the mentorship, Ícaro had succeeded in writing his pipeline in Nextflow and making it publicly available at phiflow.

phiflow diagram

Metromap of the phiflow workflow

Through all three rounds, I had the opportunity to work with some incredible people! But the awesomeness didn’t end with my mentees. One thing that always stuck out to me was how motivated everyone was, both mentees and mentors. There was a sense of excitement and real progress was being made by every group. After the first round ended, I remember thinking to myself, “how could it get better?” Haha, well it did, and it continued to get better and better in Rounds 2 and 3. I think this is a great testament to the organizers at nf-core that put it all together, the mentors and mentees, and the community behind Nextflow and nf-core.

For the future mentees in mentorship opportunities! Please don’t let yourself stop you from applying. Whether it’s a time issue, or a fear of not having enough experience to be productive. In each round, we’ve had people from all over the world, starting from the ground with no experience, to some mentees in which I wondered if maybe they should have been a mentor (some mentees did end up being a mentor in the last round!). As a mentee, it is a great opportunity to work directly with a mentor dedicated to seeing you grow and build confidence when it comes to Nextflow and bioinformatics. In addition, you will be introduced to the incredible community that is behind Nextflow and nf-core. I think you will quickly learn there are so many people in this community that are willing to help!

For the future mentors! It’s always awesome to be able to help others learn, but sometimes the mentor needs to learn too! For me, I found the nf-core Mentorship Program to be a great opportunity to improve my skills as a mentor. But it wasn’t just from working with my mentees. During each round I was surrounded by many great role models in the form of mentors and mentees to learn from. No two groups ever had the same goals, so you really get the chance to see so many different styles of mentorship being implemented, all producing significant results for each mentee. Like I told the mentees, if the opportunity comes up again, take the chance and apply to be a mentor!

There have now been three rounds of the nf-core Mentorship Program, and I am very proud to have been a mentor in each round! During this I have learned so much and been able to help my mentees and the community grow. I look forward to seeing what the future holds for the mentorship opportunities in the Nextflow community, and I encourage potential mentors and mentees to consider joining the program!

nextflow nf-core mentorship ambassador_post