Evan Floden
Evan FlodenJun 03, 2021

RNA Society Hosts APAeval Challenge on Nextflow Tower

The RNA Society is hosting APAeval, a community effort to evaluate computational methods for the detection and quantification of poly(A) sites and the estimation of their differential usage across RNA-seq samples.

The bioinformatics software landscape is highly diverse, often with dozens of tools available for the same task. For a researcher trying to make sense of their data, choosing the best tool for the particular job in hand becomes extremely daunting. Recognizing the need for independent benchmarking efforts for bioinformatics tools, the RNA Society and the iRNA COSI network have launched the APAeval Challenge, an independent community benchmarking initiative. Focusing on alternative polyadenylation (APA), APAeval benchmarks tools and methods identify, quantify, and/or determine the differential usage of alternative polyadenylation sites in RNA transcripts. Apart from serving a real community need, APAeval is meant to bring together biologists, bioinformaticians and developers to share experiences and learn from one another.

The main event is a hackathon during which attendees contribute workflows that run common poly(A) identification/quantification tools. These workflows will be written in either Nextflow or Snakemake, two of the most widely used workflow languages in the bioinformatics field. The workflows will then be run against standard preprocessed data generated by the nf-core rnaseq Nextflow pipeline. Finally, Nextflow workflows will gather the outputs of individual tools, compare them against gold standards, generate result visualizations, and integrate them into OpenEBench, a benchmarking portal operated by ELIXIR, an initiative aiming to harmonize the European life sciences infrastructure.

Seqera collaborated with the APAeval organizers to contribute access to Nextflow Tower, as well as providing a Nextflow workshop with AWS generously providing credits for compute and storage. Nextflow enables the attendees to focus on developing their workflows while Tower provides an environment to collaborate and manage workflows. Additionally, Tower Forge automatically sets up AWS Batch computing environments on demand. Utilizing the powerful and scalable AWS Batch compute capabilities is achieved with minimal user input, thus lowering the barriers for researchers.

Tower’s new Teams feature was utilized so the attendees could collaborate and easily share their workflows. Tower provides a unified way to manage users, teams, and compute resources. The Seqera team configured an APAeval organization in the hosted tower.nf environment so that the organizers simply had to add attendees who were then able to immediately begin launching workflows on AWS Batch.

“We are excited about this collaboration with the RNA Society and the APAeval team. We are pleased to give back to the community and believe this is a fantastic opportunity to showcase the new Tower capabilities of workspaces and teams in a hackathon setting“ said Paolo Di Tommaso, CTO of Seqera and creator of the Nextflow project. “Being able to run our workflows in the cloud is crucial to APAeval, given that hackathon participants work at many different institutes spread out across the globe. Being able to use Tower is really helping us a lot with that, as it considerably lowers the entry barrier to cloud computing, allowing us to launch Nextflow workflows via a convenient user interface”

Alexander Kanitz, senior scientist at the University of Basel in Switzerland and one of the co-organizers of APAeval