Nextflow and nf-core Mentorship, Round 2
Introduction
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.
Thanks to the support of our Chan Zuckerberg Initiative Diversity and Inclusion grant, we established an international Nextflow and nf-core mentoring program. With the second round of the mentorship program now complete, we celebrate the success of the most recent cohort of mentors and mentees.
From hundreds of applications, thirteen pairs of mentors and mentees were chosen for the second round of the program. For the past four months, they met regularly to collaborate on Nextflow or nf-core projects. The project scope was left up to the mentees, enabling them to work on any project aligned with their scientific interests and schedules.
Mentor-mentee pairs worked on a range of projects that included learning Nextflow and nf-core fundamentals, setting up Nextflow on their institutional clusters, translating Nextflow training material into other languages, and developing and implementing Nextflow and nf-core pipelines. Impressively, despite many mentees starting the program with very limited knowledge of Nextflow and nf-core, they completed the program with confidence and improved their abilities to develop and implement scalable and reproducible scientific workflows.
Jing Lu (Mentee) & Moritz Beber (Mentor)
Jing joined the program with the goal of learning how to develop advanced Nextflow pipelines for disease surveillance at the Guangdong Provincial Center for Diseases Control and Prevention in China. His mentor was Moritz Beber from Denmark.
Together, Jing and Moritz developed a pipeline for the analysis of SARS-CoV-2 genomes from sewage samples. They also used GitHub and docker containers to make the pipeline more sharable and reproducible. In the future, Jing hopes to use Nextflow Tower to share the pipeline with other institutions.
Luria Leslie Founou (Mentee) & Sebastian Malkusch (Mentor)
Luria's goal was to accelerate her understanding of Nextflow and apply it to her exploration of the resistome, virulome, mobilome, and phylogeny of bacteria at the Research Centre of Expertise and Biological Diagnostic of Cameroon. Luria was mentored by Sebastian Malkusch, Kolja Becker, and Alex Peltzer from the Boehringer Ingelheim Pharma GmbH & Co. KG in Germany.
For their project, Luria and her mentors developed a pipeline for mapping multi-dimensional feature space onto a discrete or continuous response variable by using multivariate models from the field of classical machine learning. Their pipeline will be able to handle classification, regression, and time-to-event models and can be used for model training, validation, and feature selection.
Sebastian Musundi (Mentee) & Athanasios Baltzis (Mentor)
Sebastian, from Mount Kenya University in Kenya, joined the mentorship program with the goal of using Nextflow pipelines to identify vaccine targets in Apicomplexan parasites. He was mentored by Athanasios Balzis from the Centre for Genomic Regulation in Spain.
With Athanasios’s help, Sebastian learned the fundamentals for developing Nextflow pipelines. During the learning process, they developed a pipeline for customized RNA sequencing and a pipeline for predicting antimicrobial resistance genes. With his new skills, Sebastian plans to keep using Nextflow on a daily basis and start contributing to nf-core.
Juan Ugalde (Mentee) & Robert Petit (Mentor)
Juan joined the mentorship program with the goal of improving his understanding of Nextflow to support microbial and viral analysis at the Universidad Andres Bello in Chile. Juan was mentored by Robert Petit from the Wyoming Public Health Laboratory in the USA. Robert is an experienced Nextflow mentor who also mentored in Round 1 of the program.
Juan and Robert shared an interest in viral genomics. After learning more about the Nextflow and nf-core ecosystem, Robert mentored Juan as he developed a Nextflow viral amplicon analysis pipeline. Juan will continue his Nextflow and nf-core journey by sharing his new knowledge with his group and incorporating it into his classes in the coming semester.
Bhargava Reddy Morampalli (Mentee) & Venkat Malladi (Mentor)
Bhargava studies at Massey University in New Zealand and joined the program with the goal of improving his understanding of Nextflow and resolving issues he was facing while developing a pipeline to analyze Nanopore direct RNA sequencing data. Bhargava was mentored by Venkat Malladi from Microsoft in the USA.
Bhargava and Venkat worked on Bhargava’s pipeline to identify RNA modifications from bacteria. Their successes included advancing the pipeline and making Singularity images for the tools Bhargava was using to make it more reproducible. For Bhargava, the mentorship program was a great kickstart for learning Nextflow and his pipeline development. He hopes to continue to develop his pipeline and optimize it for cloud platforms in the future.
Odion Ikhimiukor (Mentee) & Ben Sherman (Mentor)
Before the program, Odion, who is at the University at Albany in the USA, was new to Nextflow and nf-core. He joined the program with the goal of improving his understanding and to learn how to develop pipelines for bacterial genome analysis. His mentor Ben Sherman works for Seqera Labs in the USA.
During the program Odion and Ben developed a pipeline to analyze bacterial genomes for antimicrobial resistance surveillance. They also developed configuration settings to enable the deployment of their pipeline with high and low resources. Odion has plans to share his new knowledge with others in his community.
Batool Almarzouq (Mentee) & Murray Wham (Mentor)
Batool works at the King Abdullah International Medical Research Center in Saudi Arabia. Her goal for the mentorship program was to contribute to, and develop, nf-core pipelines. Additionally, she aimed to develop new educational resources for nf-core that can support researchers from lowly represented groups. Her mentor was Murray Wham from the University of Edinburgh in the UK.
During the mentorship program, Murray helped Batool develop her molecular dynamics pipeline and participate in the 1st Biohackathon in MENA (KAUST). Batool and Murray also found ways to make documentation more accessible and are actively promoting Nextlfow and nf-core in Saudi Arabia.
Mariama Telly Diallo (Mentee) & Emilio Garcia (Mentor)
Mariama Telly joined the mentorship program with the goal of developing and implementing Nextflow pipelines for malaria research at the Medical Research Unit at The London School of Hygiene and Tropical Medicine in Gambia. She was mentored by Emilio Garcia from Platomics in Austria. Emilio is another experienced mentor who joined the program for a second time.
Together, Mariama Telly and Emilio worked on learning the basics of Nextflow, Git, and Docker. Putting these skills into practice they started to develop a Nextflow pipeline with a docker file and custom configuration. Mariama Telly greatly improved her understanding of best practices and Nextflow and intends to use her newfound knowledge for future projects.
Anabella Trigila (Mentee) & Matthias De Smet (Mentor)
Anabella’s goal was to set up Nextflow on her institutional cluster at Héritas S.A. in Argentina and translate some bash pipelines into Nextflow pipelines. Anabella was mentored by Matthias De Smet from Ghent University in Belgium.
Anabella and Matthias worked on developing several new nf-core modules. Extending this, they started the development of a pipeline to process VCFs obtained from saliva samples and a pipeline to infer ancestry from VCF samples. Anabella has now transitioned from a user to a developer and made multiple contributions to the most recent nf-core hackathon. She also contributed to the Spanish translation of the Nextflow training material.
Juliano de Oliveira Silveira (Mentee) & Maxime Garcia (Mentor)
Juliano works at the Laboratório Central de Saúde Pública RS in Brazil. He joined the program with the goal of setting up Nextflow at his institution, which led him to learn to write his own pipelines. Juliano was mentored by Maxime Garcia from Seqera Labs in Sweden.
Juliano and Maxime worked on learning about Nextflow and nf-core. Juliano applied his new skills to an open-source bioinformatics program that used Nextflow with a customized R script. Juliano hopes to give back to the wider community and peers in Brazil.
Patricia Agudelo-Romero (Mentee) & Abhinav Sharma (Mentor)
Patricia's goal was to create, customize, and deploy nf-core pipelines at the Telethon Kids Institute in Australia. Her mentor was Abhinav Sharma from Stellenbosch University in South Africa.
Abhinav helped Patricia learn how to write reproducible pipelines with Nextflow and how to work with shared code repositories on GitHub. With Abhinav's support, Patricia worked on translating a Snakemake pipeline designed for genome virus identification and classification into Nextflow. Patricia is already applying her new skills and supporting others at her institute as they adopt Nextflow.
Mariana Guilardi (Mentee) & Alyssa Briggs (Mentor)
Mariana’s goal was to learn the fundamentals of Nextflow, construct and run pipelines, and help with nf-core pipeline development. Her mentor was Alyssa Briggs from the University of Texas at Dallas in the USA
At the start of the program, Alyssa helped Mariana learn the fundamentals of Nextflow. With Alyssa’s help, Mariana’s skills progressed rapidly and by the end of the program, they were running pipelines and developing new nf-core modules and the nf-core/viralintegration pipeline. Mariana also made community contributions to the Portuguese translation of the Nextflow training material.
Liliane Cavalcante (Mentee) & Marcel Ribeiro-Dantas (Mentor)
Liliane’s goal was to develop and apply Nextflow pipelines for genomic and epidemiological analyses at the Laboratório Central de Saúde Pública Noel Nutels in Brazil. Her mentor was Marcel Ribeiro-Dantas from Seqera Labs in Brazil.
Liliane and Marcel used Nextflow and nf-core to analyze SARS-CoV-2 genomes and demographic data for public health surveillance. They used the nf-core/viralrecon pipeline and made a new Nextflow script for additional analysis and generating graphs.
Conclusion
As with the first round of the program, the feedback about the second round of the mentorship program was overwhelmingly positive. All mentees found the experience to be highly beneficial and were grateful for the opportunity to participate.
“Having a mentor guide through the entire program was super cool. We worked all the way from the basics of Nextflow and learned a lot about developing and debugging pipelines. Today, I feel more confident than before in using Nextflow on a daily basis.” - Sebastian Musundi (Mentee)
Similarly, the mentors also found the experience to be highly rewarding.
“As a mentor, I really enjoyed participating in the program. Not only did I have the chance to support and work with colleagues from lowly represented regions, but also I learned a lot and improved myself through the mentoring and teaching process.” - Athanasios Baltzis (Mentor)
Importantly, all program participants expressed their willingness to encourage others to be part of it in the future.
“The mentorship allows mentees not only to learn nf-core/Nextflow but also a lot of aspects about open-source reproducible research. With your learning, at the end of the mentorship, you could even contribute back to the nf-core community, which is fantastic! I would tell everyone who is interested in the program to go for it.” - Anabella Trigila (Mentee)
As the Nextflow and nf-core communities continue to grow, the mentorship program will have long-lasting benefits beyond those that can be immediately measured. Mentees from the program have already become positive role models, contributing new perspectives to the broader community.
“I highly recommend this program. Independent if you are new to Nextflow or already have some experience, the possibility of working with amazing people to learn about the Nextflow ecosystem is invaluable. It helped me to improve my work, learn new things, and become confident enough to teach Nextflow to students.” - Juan Ugalde (Mentee)
We were delighted with the achievements of the mentors and mentees. Applications for the third round are now open! For more information, please visit https://nf-co.re/mentorships.