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Join us to hear Phil Ewels chat with Maxime Garciaand Franziska Bonath about how nf-core started at theNational Genomics Infrastructure (NGI) at SciLifeLab in Sweden.We chat about how the nf-core/sarek pipeline grew alongside and eventually joined nf-core,as well as the early days of nf-core bytesize talks and outreach organisation.Links:- SciLifeLab- National Genomics Infrastructure- Maxime's Nextflow Summit Boston 2023 presentation about Sarek- nf-core bytesize talks
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Tune in to hear all about Pixelgen Technologies - creators of a novel technologyfor doing single-cell spatial proteomics.
We chat about how this fascinating technology works, what you can do with the dataand why they chose to develop their analysis suite as an open-source nf-core pipeline.
Links:
Software: nf-core/pixelator pipeline Pixelator Python package Science: Nature Methods publication: “Molecular pixelation: spatial proteomics of single cells by sequencing” Presentations: Nextflow Summit 2022 talk: “Pixelgen Technologies ❤︎ Nextflow” Nextflow Summit 2024 Boston talk: “Nextflow allows Pixelgen innovation engine to reach the market quicker” Nextflow Summit 2024 Barcelona Pixelgen: Pixelgen Technologies homepage @PixelgenTech on twitter / X and LinkedIn BioLizard: BioLizard homepage @BioLizard_nv on twitter / X and LinkedInChapters:
Start (00:00) Welcome (00:09) Introductions (00:50) Intro to Pixelgen Technologies (01:41) Lab methods (03:08) Nature Methods publication (06:15) Data visualisation (09:35) Working with single cell data (12:29) Cell interactions (15:06) Why Pixelgen chose open source (16:05) Pixelator Python package (20:10) Building within nf-core (21:40) Florian - Biolizard (23:01) Pipeline overview (25:19) Using nf-core from a commercial setting (26:50) Coming out of stealth (28:53) Extending Pixelator (32:24) Dealing with customers (34:58) Looking to the future (39:38) Interactive analysis (41:32) Advice for others (43:12) Pixelgen at the Nextflow Summit (45:16) -
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Evan Floden (CEO and co-founder of Seqera) joins Phil Ewels (Product Manager for OSS at Seqera) to talk about two of the big announcements at the recent Nextflow Summit Boston 2024 - Seqera Pipelines and Seqera Containers.We dive into what these two new community offerings are, why we built them and how they work. Links:
https://seqera.io/pipelines/ https://seqera.io/containers/ Announcement blog post Nextflow Summit Boston 2024 agenda Summit YouTube playlist Nextflow 24.04 blog postTimeline:
00:00 - Introduction
00:37 - Nextflow Summit Boston 2024
01:14 - Summit talks available online
01:57 - Summit announcements
04:32 - Seqera Pipelines - motivations
05:59 - Seqera Pipelines - first look
06:48 - Testing requirements for community pipelines
10:05 - How we tested pipelines
11:53 - SRA-Explorer tangent
12:34 - Seqera Pipelines - live demo
16:14 - Getting Nextflow launch commands
19:12 - Seqera Containers - intro
24:03 - Seqera Containers - live demo
27:13 - Containers - ARM cpu arch builds
28:33 - Singularity containers
29:09 - Wave CLI
31:19 - Nextflow with Seqera Containers
33:22 - Seqera Containers - future usage
35:09 - Where to read more
36:53 - Thank you to the community
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Join us as we discuss the brand new @nf-core / EuroFaang pre-print! 🔥 We chat to some of the key authors, covering the background to the paper, the main messages and how EuroFAANG and nf-core have collaborated. 🧬 👩🏻🔬
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Join us in this episode of the Channels podcast for a closer look at the Nextflow Ambassadors Program. Marcel Ribeiro-Dantas and Geraldine Van der Auwera discuss the origins of the program, recent highlights and next steps, including the open call for new Ambassadors, which will close June 14.
Relevant links:
Call for applications: https://www.nextflow.io/ambassadors.html Original announcement: https://www.nextflow.io/blog/2023/introducing-nextflow-ambassador-program.html Marcel’s favorite Ambassador-contributed Nextflow blog post: https://www.nextflow.io/blog/2024/reflections-on-nextflow-mentorship.html -
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 Welcome00:03:27 Nextflow docs00:08:34 Starting by forking nf-hello00:10:32 Overview of project files00:17:13 Trying a first compile00:18:12 Different publishing methods00:19:54 nf-boost local publish method00:23:05 Trying the new compile00:24:00 Running locally with the plugin00:27:32 Looking at the nf-hello plugin code00:39:29 Deleting files we don't need00:42:34 Finding event names in the Nextflow source00:47:46 Writing some custom functions00:49:41 Testing our new code00:51:51 Modifying the test pipeline to create files00:54:14 Coding up the JSON output00:59:20 Looking at nf-prov code for BCO files01:05:30 Testing JSON output01:09:39 Automatic work dir cleanup / nf-boost01:12:17 Publishing a release on GitHub01:19:07 Custom plugin repositories01:26:47 Publishing for all Nextflow users01:29:52 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!
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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.
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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.
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A recap of our current training formulas, how we got here and where we’re heading to next.
Join us in this episode of the Channels podcast as Geraldine Van der Auwera and Chris Hakkaart discuss options for learning Nextflow in 2024. A recap of our current training formulas, how we got here and where we’re heading to next.
Upcoming training opportunities
Community Foundational Nextflow Training — Online, 5-6 March 2024 Training at Seqera Sessions — London, 21 March 2024 Training at Nextflow Summit — Boston, 21-22 May 2024Other upcoming events of interest
nf-core Hackathon — Online + Local Hubs, 18-20 March 2024 -
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.
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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
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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 OctoberAfter 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!
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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.
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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!
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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.
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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.
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