Ever wanted to peer inside Nextflow as it runs your pipeline? We play with an interactive debugger to do just that. Also, a first peek at a new Nextflow Ambassador program!
In this News and Views episode, Phil Ewels, Chris Hakkaart and Marcel Ribeiro-Dantas play with interactive debuggers in IntelliJ to try to understand what’s happening in their pipeline. We also give a first look at plans for a brand new “Nextflow Ambassador” program that we’ll be launching soon, as well as a revamped training course that was rescued from the precipice.
Interactive debugging
After a tip-off from a Nextflow developer and a pull-request in progress, we explore some Nextflow pipeline code using the interactive debugger in the IntelliJ IDEA code editor.
We were using Nextflow code from nextflow-io/nextflow Pull Request #3197 (specifically commit hash fcbb912).
Apologies for the confusion on air, hopefully all will soon become clear if / when the pull-request is merged and Marcel finishes his blog post!
Ambassadors
We often get questions or requests for help doing talks or local events. We’ll soon launch a new “Nextflow Ambassador” programme that we’ll be running for community heroes. Nothing is really finalized yet, so everything is very much subject to some change at this point!
We’ll be looking for people interested in writing blogs, organizing local events, presenting Nextflow at other events and generally supporting the community in any way. In return, Seqera will provide ambassadors with support for events (stickers and maybe pizza money), an insider’s look at nextflow initiatives and - most importantly of all - exclusive ambassador swag.
Applications will open soon, stay tuned for details.
Training
The “Hands on” training at https://training.nextflow.io has been rescued! It was written in DSL1 and has been on the verge of being deleted for some time. It’s now updated and ready for use.
The training describes how to create a variant calling analysis pipeline for RNA-seq data-based. It’s shorter than the Basic training (~1.5 hours, vs. 3 x 2.5 hours) and is well suited to those wanting a refresher, or who already have some knowledge about Nextflow.
We will run this training for free online in September, as one of three training sessions:
- Foundational Training: 6-8 Sept
- Hands-on: 20 Sept (web page coming soon)
- Advanced Training: 27-28 Sept
Please use the links above to register for the training events.
Nextflow Summit 2023
The call for abstracts has closed and we’ve selected our speakers! See who they are on the Summit website: https://summit.nextflow.io - the final program should be released any day now.
Keynotes will be given by Erik Garrison - Assistant Professor at the University of Tennessee Health Science Center (Barcelona) and Adam Phillippy - Senior Investigator and head of the Genome Informatics Section at the U.S. National Human Genome Research Institute (Boston).