Florian Wünnemann
@flowuenne.bsky.social
Bioinformatics engineer at Seqera (seqera.io) & Nextflow ambassador
Genomics 🧬 | Spatial omics🔬 | technology 💻 | soccer ⚽
Working towards scalable and reproducible science with #Nextflow
Living in Montreal 🇨🇦
Genomics 🧬 | Spatial omics🔬 | technology 💻 | soccer ⚽
Working towards scalable and reproducible science with #Nextflow
Living in Montreal 🇨🇦
Pinned
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...
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...
Join me today at the @nf-co.re help desk to discuss your questions about @nextflow.io and nf-core at 2pm Eastern Time! 🍏💻🧬!
🧑🏾💻 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!
📅 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!
October 7, 2025 at 2:23 PM
Join me today at the @nf-co.re help desk to discuss your questions about @nextflow.io and nf-core at 2pm Eastern Time! 🍏💻🧬!
Join us for two days of fun in Barcelona, hacking away at nf-core projects!
Spaces are filling up for the @nf-co.re Hackathon in Barcelona on Oct 28-29! 👩💻
🔗 Register now: hubs.la/Q03K3MmF0
🔗 Register now: hubs.la/Q03K3MmF0
September 19, 2025 at 3:09 PM
Join us for two days of fun in Barcelona, hacking away at nf-core projects!
Reposted by Florian Wünnemann
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
👉 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
May 9, 2025 at 7:39 AM
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
👉 Read now: hubs.la/Q03lM5KG0
#NextflowAmbassador @nf-co.re
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! 👏🤩
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...
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...
April 16, 2025 at 11:27 AM
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! 👏🤩
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! 🤩🔬🧪
🎉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
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
April 4, 2025 at 2:07 PM
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! 🤩🔬🧪
Reposted by Florian Wünnemann
My latest #Nextflow pipeline has just been published in JOSS 🎉
Just published in JOSS: 'AliNe: A Flexible and Efficient Nextflow Pipeline for Read Alignment' https://doi.org/10.21105/joss.07545
March 15, 2025 at 7:45 PM
My latest #Nextflow pipeline has just been published in JOSS 🎉
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 💵.
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
💡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
March 11, 2025 at 1:23 PM
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 💵.
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...
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...
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
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
March 10, 2025 at 3:28 PM
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...
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...
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 🤩!
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 🤩!
📢 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
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
March 5, 2025 at 2:48 PM
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 🤩!
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 🤩!
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 🚀 🤩!
💬 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 🚀 🤩!
🚀 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
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
February 26, 2025 at 1:37 PM
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 🚀 🤩!
💬 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 🚀 🤩!
Reposted by Florian Wünnemann
Interesting to see doom and gloom as separate ends of a governance axis!
February 24, 2025 at 6:24 PM
Interesting to see doom and gloom as separate ends of a governance axis!
Reposted by Florian Wünnemann
New blog post: Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper doi.org/10.59350/wzt... #Rstats
February 10, 2025 at 10:59 AM
New blog post: Exploring the bioRxiv API with R, httr2, rvest, tidytext, and Datawrapper doi.org/10.59350/wzt... #Rstats
Reposted by Florian Wünnemann
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
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
February 3, 2025 at 2:22 PM
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
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
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! 🤩
📢 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
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
January 27, 2025 at 11:52 AM
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! 🤩
Reposted by Florian Wünnemann
📣 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
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
January 26, 2025 at 2:00 PM
📣 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
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
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 !
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 !
The gold standard in #bioinformatics reporting just got even better! #AI Summaries are now available in @multiqc.info🎉
Find out more: hubs.la/Q033Kjp30
Find out more: hubs.la/Q033Kjp30
January 23, 2025 at 3:35 PM
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 !
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 !
Reposted by Florian Wünnemann
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...
January 19, 2025 at 4:40 PM
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...
Reposted by Florian Wünnemann
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities
January 14, 2025 at 2:44 PM
Are you looking for job opportunities where your #Nextflow skills are valued? Check the list we've compiled below. #Jobs #Opportunities
Reposted by Florian Wünnemann
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
January 14, 2025 at 8:37 PM
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
Reposted by Florian Wünnemann
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
January 13, 2025 at 9:00 PM
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)
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 😊!
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/...
- 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
January 8, 2025 at 4:36 PM
Do you want some AI guided help to write #Nextflow pipelines or convert your old legacy pipelines to #Nextflow? Go to seqera.io and try out Seqera AI now 🤩!
Write once, run anywhere: By wrapping your scripts to @nextflow.io, you can fully describe a computational pipeline with all of its dependencies and run it anywhere! 🧵
January 8, 2025 at 3:33 PM
Reposted by Florian Wünnemann
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing #JASMS pubs.acs.org/doi/10.1021/...
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing
Reproducibility in untargeted metabolomics data processing remains a significant challenge due to software limitations and the complex series of steps required. To address these issues, we developed N...
pubs.acs.org
January 5, 2025 at 7:20 PM
Nextflow4MS-DIAL: A Reproducible Nextflow-Based Workflow for Liquid Chromatography–Mass Spectrometry Metabolomics Data Processing #JASMS pubs.acs.org/doi/10.1021/...
For anyone that loves poker and card games, Balatro is such a great game! Just started playing it again on my tablet via Apple Arcade and having a blast 🎮🃏!
apps.apple.com/ca/app/balat...
apps.apple.com/ca/app/balat...
Balatro+
Welcome to the official Balatro+ game!
Hypnotic and endlessly satisfying, Balatro is a magical mix of card games like Solitaire and Poker, that lets you twist the rules in ways never seen before!
Yo...
apps.apple.com
January 2, 2025 at 9:05 PM
For anyone that loves poker and card games, Balatro is such a great game! Just started playing it again on my tablet via Apple Arcade and having a blast 🎮🃏!
apps.apple.com/ca/app/balat...
apps.apple.com/ca/app/balat...