Lightnews — Scholar-powered news

Florian Wünnemann

@flowuenne.bsky.social

1.5K followers 130 following 87 posts

Bioinformatics engineer at Seqera (seqera.io) & Nextflow ambassador Genomics 🧬 | Spatial omics🔬 | technology 💻 | soccer ⚽ Working towards scalable and reproducible science with #Nextflow Living in Montreal 🇨🇦

Posts Media Videos Starter Packs

Pinned

Florian Wünnemann @flowuenne.bsky.social · Dec 3

Christmas time is upon us 🎄🎅! What better way to count down the days till Christmas eve than with an Advent calender?

I am one day late, but here is little Nextflow advent calender I made for everyone. Check back every day at midnight EST to open a new door:
flowuenne.github.io/nextflow_adv...

1 6 11

Florian Wünnemann @flowuenne.bsky.social · 3d

Join me today at the @nf-co.re help desk to discuss your questions about @nextflow.io and nf-core at 2pm Eastern Time! 🍏💻🧬!

nf-core @nf-co.re · 3d

🧑🏾‍💻 Need help with #nfcore #nextflow ( #bioinformatics ) pipelines, running or developing?

📅 We host regular helpdesks for different TZs

- 🌎 Americas: Tues. @ 14:00 ET (Today)
- 🌍 Eur/M.E./Afr: Thurs. @ 10:00-11:00 CEST
- 🌏 Asia-Pacific: Weds. @ 15:00 NZDT

Join the nf-core slack for more details!

Florian Wünnemann @flowuenne.bsky.social · 20d

Join us for two days of fun in Barcelona, hacking away at nf-core projects!

Seqera @seqera.io · 21d

Spaces are filling up for the @nf-co.re Hackathon in Barcelona on Oct 28-29! 👩‍💻

🔗 Register now: hubs.la/Q03K3MmF0

Reposted by Florian Wünnemann

Nextflow @nextflow.io · May 9

Check out the blog post by Nextflow Ambassador Zohaib Anwar on VIRUS-MVP: a flexible and scalable workflow for genomic surveillance of priority viruses including SARS-CoV-2, Mpox, RSV, and influenza! 🦠

👉 Read now: hubs.la/Q03lM5KG0

#NextflowAmbassador @nf-co.re

VIRUS-MVP: A scalable and flexible pathogen surveillance workflow powered by Nextflow and nf-core | Seqera

VIRUS-MVP leverages Nextflow and nf-core to provide a modular, automated, and scalable framework for genomic surveillance of priority viruses. Designed initially for SARS-CoV-2, the workflow was later...

hubs.la

2 5

Florian Wünnemann @flowuenne.bsky.social · Apr 16

Check out this fantastic work on neighbourhood preference in spatial omics data from the Schapiro lab 🚀! Congratulations @chiaraschiller.bsky.social and team on a wonderful project! 👏🤩

Chiara Schiller @chiaraschiller.bsky.social · Apr 15

1/
Ever wondered how to best quantify cell-cell neighbor preferences in tissues?
We compared 9+ neighbor preference (NEP) methods for analysing spatial omics data and propose a novel approach that combines the most relevant analysis features which we call COZI 🔬✨

Read more: doi.org/10.1101/2025...

Schematic overview of NEP analysis steps (Neighborhood definition, Quantification and NEP score) and the systematic method performance comparison using simulated data for cohort distinction.

1 3

Florian Wünnemann @flowuenne.bsky.social · Apr 4

You should definitely check out this amazing Nextflow podcast episode with my friend and collaborator @kbestak.bsky.social discussing microscopy and spatial omics workflows in nf-core and Nextflow! 🤩🔬🧪

Nextflow @nextflow.io · Apr 4

🎉Episode 50 of the @nextflow.io Podcast is here!

Host @ewels.bsky.social sits down with @kbestak.bsky.social, a PhD student and active contributor to the @nf-co.re community, working at the cutting edge of #SpatialOmics and #microscopy.

🎧Catch it here: hubs.la/Q03fVPNx0

Imaging pipelines and analysis, with Krešimir Beštak | The Nextflow Podcast by Seqera

Seqera | The Home for Open Science | From the creators of Nextflow, Wave, and MultiQC

hubs.la

Florian Wünnemann @flowuenne.bsky.social · Mar 19

Glad you enjoyed the training, thanks for attending and the shoutout here @mragsac.com! Always happy to show how #Nextflow works to people and how they can benefit from using it.

For anyone that wants to use the training materials, they are available at training.nextflow.io!

nextflow.tr

2 1

Reposted by Florian Wünnemann

Jacques Dainat @jacquesdainat.bsky.social · Mar 15

My latest #Nextflow pipeline has just been published in JOSS 🎉

Journal of Open Source Software @joss-openjournals.bsky.social · Mar 15

Just published in JOSS: 'AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment' https://doi.org/10.21105/joss.07545

2 2

Florian Wünnemann @flowuenne.bsky.social · Mar 11

Running Nextflow pipelines on AWS ☁️? Check out the blogpost I wrote about using resource Labels with Nextflow and Seqera to get detailed pipeline run costs 💵.

Seqera @seqera.io · Mar 11

Cost reporting of computational projects and workflows is critical for understanding and optimizing cloud spending

💡Our latest blog explores how resource labels can be used to tag AWS infrastructure resources for detailed cost reporting across your workflows and teams in Seqera

hubs.la/Q03bghM70

How utilizing resource labels on Seqera can help with high resolution cost analysis in AWS

This blog post provides a step-by-step guide to setting up and understanding resource labels within Seqera Platform and how they can be used to tag AWS infrastructure resources for detailed cost reporting across your workflows and teams.

hubs.la

Florian Wünnemann @flowuenne.bsky.social · Mar 10

Major heartbreak when it happened. Reminded everytime I watch the movies 😭. Guess no one ran around with "Hedwig dies on page xxx" shirts at the time to spoil you 😉

1 1

Florian Wünnemann @flowuenne.bsky.social · Mar 10

If you want to start learning #Nextflow or brush up on your basics of #Nextflow, now is the perfect time 🕑!

New training materials and support from ambassadors and experienced community members during training week help guide you through it, at your own pace!
community.seqera.io/t/nextflow-t...

Nextflow @nextflow.io · Mar 10

The #Nextflow #Training week has begun! 🎉

New to Nextflow or need a guided intro? Watch the brand new on-demand walkthrough videos for the "Hello Nextflow" course, and learn at your own pace!

hubs.la/Q03b2-Rk0

Hello Nextflow: Intro and setup

Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

hubs.la

3 7

Florian Wünnemann @flowuenne.bsky.social · Mar 5

Come and talk about your amazing projects at the #Nextflow summit in Boston 🎤!

I am very sad to miss this summit this year, but it will be a fantastic event, so make sure you to submit your abstract before the deadline 🤩!

Nextflow @nextflow.io · Mar 5

📢 Reminder! The call for speakers at #NextflowSummit in Boston closes on Friday, Mar 14

Have groundbreaking research, novel workflows, or real-world success stories to share? This is your chance to take the stage!

⏳Submit your abstract now: hubs.la/Q039nrrG0

Florian Wünnemann @flowuenne.bsky.social · Feb 26

Great opportunity to get together with your colleagues and friends and watch the training videos to learn Nextflow together 👥.

💬 Discussing things not clear to you and sending questions to the community forum are all great ways to accelerate your learning experience and increase the fun 🚀 🤩!

Nextflow @nextflow.io · Feb 26

🚀 Introducing #Nextflow Training Week!

A free, self-paced online training designed to help beginners get started with Nextflow.

📅 March 10-14, 2025
🎥 On-demand videos and real-time support
💬 Ask questions in our community forum

Learn more and join us: hubs.la/Q038kTQm0

Nextflow Training Week (2025-Q1)

🚀 Nextflow Training Week is a new quarterly self-paced online training designed for accessibility and flexibility. Featuring on-demand walkthrough videos and near real-time support via the community f...

community.seqera.io

Reposted by Florian Wünnemann

Christina Agapakis @agapakis.com · Feb 24

Interesting to see doom and gloom as separate ends of a governance axis!

Sebastian S. Cocioba @atinygreencell.bsky.social · Feb 24

On the axis of doom and gloom

1 2 8

Reposted by Florian Wünnemann

Stephen Turner @stephenturner.us · Feb 10

New blog post: Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper doi.org/10.59350/wzt... #Rstats

1 6 29

Reposted by Florian Wünnemann

Jasmine Plummer @jasmineplummer.bsky.social · Feb 3

Introducing @gestaltsp.bsky.social
We’re growing with already >1000 members.
Come be part of spatial omics revolution!!! @ioavlachos.bsky.social @lgmartelotto.bsky.social @naturegenet.bsky.social rdcu.be/d8qHT
#spatial #omics #technology #computation #tissue #singlecell

Introducing the Global Alliance for Spatial Technologies (GESTALT)

Nature Genetics - This Comment outlines the creation of the Global Alliance for Spatial Technologies (GESTALT), a collaborative initiative aimed at fostering the growth and standardization of...

rdcu.be

4 8

Florian Wünnemann @flowuenne.bsky.social · Jan 27

Don't miss this chance to listen to my amazing colleagues Esha and Rob talk about how you can utilize Seqera Platform to help streamline your scientific data analysis! 🤩

Seqera @seqera.io · Jan 27

📢 Last chance to register for our webinar happening tomorrow!

Join us to discover how Seqera is streamlining the entire data lifecycle, from pipeline runs through to downstream analysis and scientific insights.

Register now: hubs.la/Q034273k0

Reposted by Florian Wünnemann

Satoshi Yoshiji, MD, PhD @satoshiyoshiji.bsky.social · Jan 26

📣 We are hiring!
Join Yoshiji Lab at McGill University Dept of Human Genetics in Montreal, Canada!
yoshiji-lab.org/joinus
✅Fully Funded Positions
• 2 MSc Students
• 1 PhD Student
• 1 Postdoc
✅Goal: Using human genetics and multi-omics for drug target discovery and precision medicine

1 4 9

Reposted by Florian Wünnemann

econmaett @econmaett.github.io · Jan 25

I think I found the talk. Thanks for the recommendation and for sharing your experience! 🙏

youtu.be/2DbuqYKOsrY?...

Nicola Rennie: Styling Quarto PDFs with Typst

YouTube video by Jumping Rivers

youtu.be

1 3 12

Florian Wünnemann @flowuenne.bsky.social · Jan 23

You can now use Seqera AI with MultiQC! 🤖

Get insights from your reports and chat about potential QC issues with Seqera AI, directly from inside your MultiQC reports! Fantastic new update by everyone involved at @seqera.io !

Seqera @seqera.io · Jan 23

The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉

Find out more: hubs.la/Q033Kjp30

Reposted by Florian Wünnemann

Diego del Alamo @delalamo.xyz · Jan 19

Protein backbone diffusion models consistently undersample catalytically important motifs, and oversample idealized helices, raising questions about the appropriateness of these methods in designing starting points for enzyme design & evolution. From www.biorxiv.org/content/10.1...

Protein structure embeddings reveal undersampled and de novo structure space. (B) First two principal components of mean-pooled ESM3 embeddings colored by helix content determined by DSSP. The indicated dashed guide lines denote visual boundaries of native structure space not sampled (Undersampled) and novel regions of protein structure for this space only observed in samples but not in native structures (De novo). (C) Rasterized visualization of panel B with 16 equally spaced grid squares in each principal component axis. A representative structure from each grid was chosen at random. Empty grid squares indicate the absence of any structure in the enclosed region. De novo alpha helices are shaded along the lower-right diagonal and the structures from CATH which do not have corresponding structures in the samples are shaded along the left and top rims. The structures are displayed in CATH raster plot are given in the Supplementary Information.

2 16 86

Florian Wünnemann @flowuenne.bsky.social · Jan 17

That looks amazing, congrats @sunjaelee.bsky.social 👏! Is the code to make the sankey diagrams available somewhere? Would love to play around with that 🤩!

1 2

Reposted by Florian Wünnemann

Nextflow @nextflow.io · Jan 14

Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities

1 3 2

Reposted by Florian Wünnemann

Piet @drpiet.bsky.social · Jan 14

Extra! Extra! If you're into cardiovascular development and regeneration, and you want to hobnob with all them awesome scientists, then follow @weinsteinconf.bsky.social and submit an abstract for the 2025 Weinstein Conference in Milwaukee!! #favorite #conference #ever

1 2

Reposted by Florian Wünnemann

Stephen Turner @stephenturner.us · Jan 13

Interesting concept. jetty::run() executes R code in a Docker container and passes the results back into the local environment https://cran.r-project.org/web/packages/jetty/index.html (source: https://github.com/dmolitor/jetty)

jetty: Execute R in a 'Docker' Context

The goal of 'jetty' is to execute R functions and code snippets in an isolated R subprocess within a 'Docker' container and return the evaluated results to the local R session. 'jetty' can install…

cran.r-project.org

1 3 17

Florian Wünnemann @flowuenne.bsky.social · Jan 8

I am organizing a local site in Montreal for this @nf-co.re hackathon 🇨🇦. Anyone in the area who is interested to help organize or join this hackathon and a potential #Nextflow training before, please DM me 😊!

nf-core @nf-co.re · Dec 19

Our next hackathon is rapidly approaching! 🚀

- March 24-26, 2025
- Online / local distributed sites

For the distributed sites, WE NEED YOU! 🎯

If you're able to book a meeting room and host a local site, fill in the local site registration form:

nf-co.re/events/2025/...

Hackathon - March 2025 (Online / Distributed)

A virtual hackathon with local sites to develop nf-core together

nf-co.re

1 5