nf-cast - the bioinformatics podcast
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Bioinformatics is advancing at a rapid pace and plays a vital role in the research, as well as the development of new targeted medications, personalized healthcare, and delivering better clinical outcomes. In this podcast, Rob Lalonde of Seqera discusses advancements at the intersection of biology and informatics with some of the world's leading bioinformaticians and data scientists.
nf-cast - the bioinformatics podcast
1w ago
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 ..read more
nf-cast - the bioinformatics podcast
3w ago
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 ..read more
nf-cast - the bioinformatics podcast
1M ago
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 ..read more
nf-cast - the bioinformatics podcast
1M ago
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 ..read more
nf-cast - the bioinformatics podcast
2M ago
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 2024
Other upcoming events of interest
nf-core Hacka ..read more
nf-cast - the bioinformatics podcast
2M ago
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 ..read more
nf-cast - the bioinformatics podcast
3M ago
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 ..read more
nf-cast - the bioinformatics podcast
3M ago
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 ..read more
nf-cast - the bioinformatics podcast
4M ago
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, B ..read more
nf-cast - the bioinformatics podcast
5M ago
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 ..read more