Channels - the nextflow podcast

This podcast episode is quite different to normal. Rather than an interview or a discussion, you'll get to watch as Ben Sherman guides Phil Ewels through the process of creating a new Nextflow Plugin from scratch. Right from the first line of code to creating a release and publishing the plugin. Nextflow plugins have been getting more attention lately and we've been getting a lot of questions in the community. There is better documentation and resources planned, but in the mean time we hope that this can be a useful guide for anyone curious in how they work, and interested in getting started. After this we will be back to our usual routine in the podcast, but we'd love to hear what you thought of this taster!

• 00:00:00 Welcome
• 00:03:27 Nextflow docs
• 00:08:34 Starting by forking nf-hello
• 00:10:32 Overview of project files
• 00:17:13 Trying a first compile
• 00:18:12 Different publishing methods
• 00:19:54 nf-boost local publish method
• 00:23:05 Trying the new compile
• 00:24:00 Running locally with the plugin
• 00:27:32 Looking at the nf-hello plugin code
• 00:39:29 Deleting files we don't need
• 00:42:34 Finding event names in the Nextflow source
• 00:47:46 Writing some custom functions
• 00:49:41 Testing our new code
• 00:51:51 Modifying the test pipeline to create files
• 00:54:14 Coding up the JSON output
• 00:59:20 Looking at nf-prov code for BCO files
• 01:05:30 Testing JSON output
• 01:09:39 Automatic work dir cleanup / nf-boost
• 01:12:17 Publishing a release on GitHub
• 01:19:07 Custom plugin repositories
• 01:26:47 Publishing for all Nextflow users
• 01:29:52 Conclusion and end

In this episode of Channels, we talk to Jakob Zeitler - Head of R&D at Matterhorn Studios. We dive into how they use Nextflow and Seqera Platform for material science research, paving the way for cheaper and more eco-friendly products for the future ⚗️👩🏻‍🔬🔬🌎 It may not be bioinformatics, but there's a lot that's in common!

In this episode of the podcast, Geraldine and Ben talk about the Global Alliance for Genomics and Health (GA4GH) and its efforts to develop interoperability standards for pipelining infrastructure. If the words TES, WES, TRS and DRS are just as much alphabet soup to you, tune in to learn all about how organizations around the world are collaborating to streamline the process of sharing and analyzing data at scale.

In this episode of Channels, we talk to Josh Chorlton - CTO & cofounder of BugSeq Bioinformatics Inc. We talk about how BugSeq got into using Nextflow and MultiQC and the tips and tricks that they've employed to push scale and performace of their tools to the limit. We cover topics like testing and CI/CD, passing around structured data objects between Groovy and Python using Protobufs, building Docker images at scale and the ins and outs of using MultiQC for custom clinical data reports.

In this episode of Channels, we talk to Paolo Di Tommaso (creator of Nextflow, Seqera CTO & cofounder) and Jordi Deu Pons (software engineer @ Seqera) about Fusion - a file system written specifically for Nextflow.

Join us in this episode of the Channels podcast to get a recap of some of the biggest features to be added to Nextflow in 2023 and take a look at some of the things coming in 2024.

We tried to do this in Episode 27 but ended up spending nearly all the time discussing community and nf-core, so this episode is dedicated to just Nextflow features.

We cover Phil's top hits:

• 2023
  • Fusion support on Azure Batch, Google Batch, SLURM, LSF
  • Spack integration
  • Markdown docs, developer docs
  • New `nextflow inspect` command
  • Channel "topics"
  • AWS Fargate for compute tasks
• 2024
  • Job arrays
  • Garbage collection (aka work directory cleanup)
  • Command line interface v2
  • Improvements to Nextflow packaging
  • Workflow inputs and outputs schema
  • Module configuration / config v2

Rob Lalonde of Seqera interviews Kelsey Florek, Senior Genomics and Data Scientist at the Wisconsin State Laboratory of Hygiene. In this interview, Rob and Kelsey discuss how genomic surveillance has changed since the COVID pandemic, and how Seqera Platform and Nextflow pipelines have substantially lowered the barrier to entry for bioinformaticians running workflows in public health labs and in the field. The viralrecon pipeline Kelsey mentioned in the interview can be found at https://nf-co.re/viralrecon

Today in the Channels podcast, we're talking about what happened this year in the Nextflow world, with particular emphasis on the many exciting developments in nf-core. We cover: - Community growth (with stats and graphs!) - The evolution of nf-core governance - The latest crop of nf-core pipelines that saw their first release this year and the expansion into domains beyond genomics (even beyond biology!) - Infrastructure updates including subworkflows and testing with nf-test - Community updates including mentorships and training - Upcoming events in 2024: nf-core online hackathon in March, Boston Summit in May and Barcelona Summit in October After today’s episode, we’ll be going on break for the winter holiday and will return in January 2024 with a fun mix of topics. Stay tuned!

In a special edition of the Channels Podcast, Geraldine Van der Auwera interviews four members of the Nextflow community attending the 2023 nf-core hackathon: Raquel Manzano, Edmund Miller, Rieke Hanssen and Francesco Lescai. Recorded in-person at the Nextflow Summit Barcelona, we hear a bit about what they have been working on, how they came to use Nextflow and what motivated them to join the nf-core hackathon.

In a special edition of the Channels Podcast, Phil Ewels chats to Geraldine Van der Auwera! Recorded in-person at the Nextflow Summit Barcelona, we hear a bit about Geraldine’s background - her work at the Broad with GATK and WDL, and the path that brought her to Seqera and the Nextflow community. Oh, and the WDL runner whose name got away is miniWDL, by Mike Lin!

Today in the Channels podcast, we're talking about computing resources... Ben Sherman takes us through new and upcoming runtime improvements in the Nextflow, leading to better performance fine tuning and simpler syntax for pipelines.

We cover:

• Fractional CPU requests
• resourceLimits directive (to replace check_max)
• Virtual threads in Groovy
• WebAssembly runtime (a lightweight alternative to containers)

Software containers using Docker / Singularity are a core part of modern data science, found at the heart of Nextflow pipelines. On today's show, we bring on the creator of Nextflow – Paolo Di Tommaso – to tell us the good, the bad and the ugly of containers.

He talks about "Wave", one of the newest tools to come out of Seqera Labs and how this can make Nextflow pipelines scale on the cloud, work behind closed doors in protected environments and how it can build & augment images with additional requirements on the fly. And all this whilst reducing the amount of boilerplate code required within your pipeline.

As if that wasn't enough, we get a live demo of Wavelit - the open source command-line interface tool, that allows you to leverage the full power of Wave as a stand-alone tool, outside of Nextflow.

In this episode of the Channels podcast, it’s all about developer experience! Ben Sherman takes us through new and upcoming language improvements in the Nextflow language which will help people writing Nextflow pipelines write code faster, with fewer errors, and of course with beautifully formatted indentation 🤩

We cover:

• What exactly was happening in the last episode, when Marcel, Chris and Phil ran wild with a beta version of breakpoint debugging in IntelliJ IDEA.
• Why informative error messages are difficult in Nextflow, and how we’re making things better (coming to your console in the next stable release!)
• How we’re building a Nextflow language server, for linting, formatting and code completion in your favourite IDE.

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, plus a revamped hands-on Nextflow training course.

In this episode of the Channels podcast we have Evan Floden (Seqera Labs CEO) and Harshil Patel (head of scientific development at Seqera Labs) on the show! We talk about: 0:00 - Introduction 1:42 - History of automated testing in nf-core 4:10 - Using Tower CLI with GitHub actions in nf-core 5:09 - Coverage of full-size tests in nf-core 8:00 - Nextflow Tower "pipeline showcase" automation 14:18 - Python library for Tower automation (tw-pywrap) 18:23 - Seqera roadmap: pipeline detail view and run linking 22:06 - Nextflow Tower - Data Explorer 28:01 - Nextflow Tower - Datasets 31:55 - Upcoming events 35:15 - Wrap up

In today's episode of the Channels Podcast, we talk to Seqera software engineer Ben Sherman about what's going on "under the hood" with Nextflow. We touch on task provenance, cloud cache databases and task / sub-workflow grouping. Gotta cache 'em all! 0:00 - Introduction 2:21 - Task provenance 14:32 - Difference to the nf-prov plugin 17:13 - Quilt packages 22:30 - Cloud cache database 32:16 - Task grouping (horizontal) 45:18 - Workflow grouping (vertical) 1:00:22 - Upcoming events 1:03:31 - Close

In this News and Views episode, Chris Hakkaart and Marcel Ribeiro-Dantas talk to Rob Syme about the exciting new Nextflow training material and ways to learn Nextflow in 2023.

In this "News & Views" episode of Channels we talk to Nextflow developer Ben Sherman about some exciting new language features (hopefully) coming soon to Nextflow:
0:00 - Introduction
2:42 - Default values for process inputs
11:59 - Arity, nullable options for input and output paths
28:17 - Named arguments for processes and workflows
36:16 - Map inputs/outputs for processes
41:14 - Custom record inputs/outputs for processes
51:37 - New community content and upcoming events

Tune to to Episode 16 of the Channels podcast to hear from the nf-core community infrastructure team: Matthias Hörtenhuber and Júlia Mir Pedrol. In a bumper episode, we discuss the new "nf-validation" Nextflow plugin (https://nextflow-io.github.io/nf-validation/) and talk nf-core components: modules and subworkflows.

In this News and Views episode, Phil Ewels talks to Ben Sherman about upcoming features in core Nextflow development: a new CLI v2 interface; submission of job arrays and intermediate file cleanup during runs.

In this "News & Views" episode of Channels we kick off the Summer 2023 series of Channels podcasts and go through some of the highlights from the latest Nextflow releases.

A special edition of Channels, Phil Ewels talks to Paolo Di Tommaso and Evan Floden about the past, present and future of Nextflow as the project celebrates its 10th anniversary.

In this "News & Views" episode of Channels we talk about improvements to handling S3 file names, support for the Spack package manager, and local hackathon sites.

In this "News & Views" episode of Channels we talk about the new Sarus container engine, staging outputs using 'rclone' and 'fcp', and using GITHUB_TOKEN to access private repositories.

In this "News & Views" episode of Channels we talk about the new Flux executor for Nextflow, the initiative to add transcripts to all nf-core bytesize videos,  and some improvements for error messaging when using Nextflow.

In this "News & Views" episode of Channels we talk about how support for Nextflow DSL1 is going to be dropped and what that means for you. We also explore the wondrous world of AI and ML with a few examples of recent pipelines we've written.

The second "News & Views" episode of Channels - join us as we chat about the nf-test framework for testing Nextflow pipelines, the second round of the Nextflow & nf-core mentorship program and a new Nextflow blog post about how to figure out exactly why your pipeline won't resume!

Rob Lalonde of Seqera Labs interviews Robert Petit, a senior bioinformatics scientist at Wyoming Public Health Laboratory. In this interview, Rob and Rob discuss public health challenges unique to Wyoming, genomic surveillance, the Bactopia pipeline, and the latest fashion trends among leading bioinformaticians in the state.

The first episode of a new format - meet Channels: the nextflow podcast. We'll be joining Rob Lalonde in bringing podcast episodes to your feeds with short News & Views episodes where you can hear us discuss hot topics in the Nextflow community.

In this Podcast, Rob Lalonde of Seqera Labs speaks with Dr. Evan Floden, CEO and co-founder of Seqera Labs. Rob and Evan talk about the history of Nextflow, breaking bad, and the future of bioinformatics. Evan also provides a live demo of Nextflow Tower.

In this Podcast, Rob Lalonde of Seqera Labs speaks with Cedric Notredame, head of the Notredame Lab at the Centre for Genomic Regulation in Barcelona, Spain. In this far-ranging discussion, Rob and Cedric talk about cloud, pipelines, and trace the evolution of Nextflow from its early days as a research project to its current role in the global COVID effort.

In this Podcast, Rob Lalonde of Seqera Labs speaks with Lorena Pantano, head of Computational Biology at NextRNA, a firm leading the next revolution in RNA-directed therapeutics located in Cambridge, Massachusetts. In this fascinating discussion, Rob and Lorena talk Bioinformatics, life in a startup, and women in technology.

In this Podcast, Rob Lalonde speaks with Nils Homer, founding partner at Fulcrum Genomics. Nils shares his unique perspectives on breaking into the bioinformatics industry, advances in technology and tools, and what to expect in the next three to five years.

In this Podcast, Rob Lalonde speaks with Phil Ewels of SciLifeLab Sweden, part of NGI Stockholm. In this fascinating discussion, they cover everything from nf-core to future bioinformatics challenges.