Lukas Forer
@lukfor.bsky.social
Assistant Professor of Genome Informatics. MedUni Innsbruck. Cloud Computing, Machine Learning, AI, Genotype Imputation. Open Source and Open Science. Co-Creator of Michigan Imputation Server and www.askimed.com. Creator of www.nf-test.com.
Pinned
Lukas Forer
@lukfor.bsky.social
· Nov 18
I just created a starter pack to collect accounts related to science in Innsbruck 🏔️
Feel free to contact me if I should put someone on the list
go.bsky.app/PTnZKvx
cc: @sigridneuhauser.bsky.social @francescafinotello.bsky.social
Feel free to contact me if I should put someone on the list
go.bsky.app/PTnZKvx
cc: @sigridneuhauser.bsky.social @francescafinotello.bsky.social
Reposted by Lukas Forer
This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...
Cameron Patrick - Some Quarto PDF formatting tips, with particular reference to thesis writing
I’ve just spent most of a day faffing around trying to get Quarto to produce a nice PDF file that I like the look of and which meets my university’s formatting requirements for a PhD thesis. Maybe my ...
cameronpatrick.com
October 3, 2025 at 11:39 PM
This is how I integrate Quarto and Zotero with minimal suffering (long rambling post, scroll down to the section on bibliography or search for Zotero): cameronpatrick.com/post/2023/07...
Reposted by Lukas Forer
Another Bactopia update!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
August 26, 2025 at 7:44 PM
Another Bactopia update!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
I think the plugin is completed now! I've also started the transition from pytest to nf-test (from @lukfor.bsky.social and @sebschoenherr.bsky.social). So far nf-test has been great to work with! Haha probably should have made the transition a long time ago!
Reposted by Lukas Forer
July 27, 2025 at 6:57 PM
Reposted by Lukas Forer
As a post-GWAS analysis, ever thought about automatic haplotype testing @ each locus + test vs any number of traits?
👏 Amazing @dariushghasemi.bsky.social just released #Haplomics, a #Snakemake pipeline walking u all the way down to summary stats+clustering
www.medrxiv.org/content/10.1...
#statgen
👏 Amazing @dariushghasemi.bsky.social just released #Haplomics, a #Snakemake pipeline walking u all the way down to summary stats+clustering
www.medrxiv.org/content/10.1...
#statgen
Haplomics: A Snakemake pipeline for haplotype-based association analysis in multi-omics studies
Summary Genome-wide association studies (GWAS) generated thousands of loci associated with complex traits and diseases. However, to characterize of the pleiotropic, molecular and population genetic bo...
www.medrxiv.org
June 13, 2025 at 7:11 AM
As a post-GWAS analysis, ever thought about automatic haplotype testing @ each locus + test vs any number of traits?
👏 Amazing @dariushghasemi.bsky.social just released #Haplomics, a #Snakemake pipeline walking u all the way down to summary stats+clustering
www.medrxiv.org/content/10.1...
#statgen
👏 Amazing @dariushghasemi.bsky.social just released #Haplomics, a #Snakemake pipeline walking u all the way down to summary stats+clustering
www.medrxiv.org/content/10.1...
#statgen
Really cool that the latest VSCode extension for Nextflow shows nf-test test coverage! 🚀
Big updates for the Nextflow @vscode.dev extension! 🚀
🔍 Workflow view – Visualize logical structure of pipelines
⚙️ Process view – See all processes in one place
🌐 Seqera view – Manage connected CEs directly in the IDE
📚 Resources view – Quickly access Copilot, AI tools & training
🔍 Workflow view – Visualize logical structure of pipelines
⚙️ Process view – See all processes in one place
🌐 Seqera view – Manage connected CEs directly in the IDE
📚 Resources view – Quickly access Copilot, AI tools & training
April 17, 2025 at 9:06 PM
Really cool that the latest VSCode extension for Nextflow shows nf-test test coverage! 🚀
Reposted by Lukas Forer
𝐇𝐮𝐦𝐚𝐧𝐠𝐞𝐧𝐨𝐦 𝐀𝐮𝐬𝐭𝐫𝐢𝐚 ist jetzt auf Bluesky!
Das österreichische Humangenomprojekt ist eine Initiative für 𝐝𝐢𝐞 𝐈𝐧𝐭𝐞𝐠𝐫𝐚𝐭𝐢𝐨𝐧 𝐠𝐞𝐧𝐞𝐭𝐢𝐬𝐜𝐡𝐞𝐫 𝐮𝐧𝐝 𝐠𝐞𝐧𝐨𝐦𝐢𝐬𝐜𝐡𝐞𝐫 𝐃𝐚𝐭𝐞𝐧 𝐢𝐧 𝐌𝐞𝐝𝐢𝐳𝐢𝐧 𝐮𝐧𝐝 𝐖𝐢𝐬𝐬𝐞𝐧𝐬𝐜𝐡𝐚𝐟𝐭 in ganz Österreich.
Infos ➡️ www.humangenom.at
#Genetik #Genetics #Health #Genomics #GenomeOfEurope
Das österreichische Humangenomprojekt ist eine Initiative für 𝐝𝐢𝐞 𝐈𝐧𝐭𝐞𝐠𝐫𝐚𝐭𝐢𝐨𝐧 𝐠𝐞𝐧𝐞𝐭𝐢𝐬𝐜𝐡𝐞𝐫 𝐮𝐧𝐝 𝐠𝐞𝐧𝐨𝐦𝐢𝐬𝐜𝐡𝐞𝐫 𝐃𝐚𝐭𝐞𝐧 𝐢𝐧 𝐌𝐞𝐝𝐢𝐳𝐢𝐧 𝐮𝐧𝐝 𝐖𝐢𝐬𝐬𝐞𝐧𝐬𝐜𝐡𝐚𝐟𝐭 in ganz Österreich.
Infos ➡️ www.humangenom.at
#Genetik #Genetics #Health #Genomics #GenomeOfEurope
March 13, 2025 at 11:04 AM
𝐇𝐮𝐦𝐚𝐧𝐠𝐞𝐧𝐨𝐦 𝐀𝐮𝐬𝐭𝐫𝐢𝐚 ist jetzt auf Bluesky!
Das österreichische Humangenomprojekt ist eine Initiative für 𝐝𝐢𝐞 𝐈𝐧𝐭𝐞𝐠𝐫𝐚𝐭𝐢𝐨𝐧 𝐠𝐞𝐧𝐞𝐭𝐢𝐬𝐜𝐡𝐞𝐫 𝐮𝐧𝐝 𝐠𝐞𝐧𝐨𝐦𝐢𝐬𝐜𝐡𝐞𝐫 𝐃𝐚𝐭𝐞𝐧 𝐢𝐧 𝐌𝐞𝐝𝐢𝐳𝐢𝐧 𝐮𝐧𝐝 𝐖𝐢𝐬𝐬𝐞𝐧𝐬𝐜𝐡𝐚𝐟𝐭 in ganz Österreich.
Infos ➡️ www.humangenom.at
#Genetik #Genetics #Health #Genomics #GenomeOfEurope
Das österreichische Humangenomprojekt ist eine Initiative für 𝐝𝐢𝐞 𝐈𝐧𝐭𝐞𝐠𝐫𝐚𝐭𝐢𝐨𝐧 𝐠𝐞𝐧𝐞𝐭𝐢𝐬𝐜𝐡𝐞𝐫 𝐮𝐧𝐝 𝐠𝐞𝐧𝐨𝐦𝐢𝐬𝐜𝐡𝐞𝐫 𝐃𝐚𝐭𝐞𝐧 𝐢𝐧 𝐌𝐞𝐝𝐢𝐳𝐢𝐧 𝐮𝐧𝐝 𝐖𝐢𝐬𝐬𝐞𝐧𝐬𝐜𝐡𝐚𝐟𝐭 in ganz Österreich.
Infos ➡️ www.humangenom.at
#Genetik #Genetics #Health #Genomics #GenomeOfEurope
Reposted by Lukas Forer
What a fantastic talk given by Prof. Michael Moor. Thanks to the Faculty of AI and Scientific Computing in Medicine for organizing such an important event. @i-med.ac.at @sebschoenherr.bsky.social @lukfor.bsky.social #MedSky
March 6, 2025 at 1:51 PM
What a fantastic talk given by Prof. Michael Moor. Thanks to the Faculty of AI and Scientific Computing in Medicine for organizing such an important event. @i-med.ac.at @sebschoenherr.bsky.social @lukfor.bsky.social #MedSky
Reposted by Lukas Forer
“Infinite code = infinite maintenance” leaddev.com/software-qua...
How AI generated code compounds technical debt
GitClear’s latest report exposes rising code duplication and declining quality as AI coding tools gain in popularity.
leaddev.com
February 23, 2025 at 11:43 AM
“Infinite code = infinite maintenance” leaddev.com/software-qua...
Reposted by Lukas Forer
🎙️ #Atherotalk Episode 7 is live, don’t miss it! I had the chance to interview my mentor, Prof. Kronenberg. @i-med.ac.at @aspcardio.bsky.social @katioorni.bsky.social
#MedSky #CardioSky #Lpa #FH #Podcast
🎧Spotify: open.spotify.com/episode/26Me...
#MedSky #CardioSky #Lpa #FH #Podcast
🎧Spotify: open.spotify.com/episode/26Me...
February 18, 2025 at 11:54 PM
🎙️ #Atherotalk Episode 7 is live, don’t miss it! I had the chance to interview my mentor, Prof. Kronenberg. @i-med.ac.at @aspcardio.bsky.social @katioorni.bsky.social
#MedSky #CardioSky #Lpa #FH #Podcast
🎧Spotify: open.spotify.com/episode/26Me...
#MedSky #CardioSky #Lpa #FH #Podcast
🎧Spotify: open.spotify.com/episode/26Me...
Just found my first real game on some old floppy discs from around 1999: a Mastermind clone written in QBasic.
I remember being super happy and proud because it was the first project I actually finished instead of stopping halfway to start another idea. 👨🏻💻
I remember being super happy and proud because it was the first project I actually finished instead of stopping halfway to start another idea. 👨🏻💻
February 15, 2025 at 9:46 AM
Just found my first real game on some old floppy discs from around 1999: a Mastermind clone written in QBasic.
I remember being super happy and proud because it was the first project I actually finished instead of stopping halfway to start another idea. 👨🏻💻
I remember being super happy and proud because it was the first project I actually finished instead of stopping halfway to start another idea. 👨🏻💻
Reposted by Lukas Forer
I'd like to share DSO, a command line helper to build reproducible data science projects with ease.
It is an opinionated way to organize data science projects, built around data version control (DVC).
github.com/Boehringer-I...
It is an opinionated way to organize data science projects, built around data version control (DVC).
github.com/Boehringer-I...
GitHub - Boehringer-Ingelheim/dso: Data Science Operations (dso) command line tool
Data Science Operations (dso) command line tool. Contribute to Boehringer-Ingelheim/dso development by creating an account on GitHub.
github.com
February 5, 2025 at 6:32 PM
I'd like to share DSO, a command line helper to build reproducible data science projects with ease.
It is an opinionated way to organize data science projects, built around data version control (DVC).
github.com/Boehringer-I...
It is an opinionated way to organize data science projects, built around data version control (DVC).
github.com/Boehringer-I...
We had an amazing time at the 2-day Hackathon at @i-med.ac.at ! Can't wait for the next one! 🚀
Very productive day 1 at the 2nd Workshop & Hackathon of Nextflow In Genomics in Innsbruck #nf-genomics #imputation-server
February 1, 2025 at 1:18 PM
We had an amazing time at the 2-day Hackathon at @i-med.ac.at ! Can't wait for the next one! 🚀
Reposted by Lukas Forer
Our Nextflow in Genomics workshop kicks off tomorrow!
Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social
#nf-genomics #freeimputation
Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social
#nf-genomics #freeimputation
January 29, 2025 at 9:04 PM
Our Nextflow in Genomics workshop kicks off tomorrow!
Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social
#nf-genomics #freeimputation
Excited to dive into imputation with @sebschoenherr.bsky.social and @lukfor.bsky.social
#nf-genomics #freeimputation
Looking forward to great discussions, learning, and sharing insights. Busy but productive days ahead!
🚀 Ready to kick off our Nextflow in Genomics workshop tomorrow at @i-med.ac.at!
🎉 Together with @lukfor.bsky.social & @silvidm.bsky.social we'll work on improving imputation server workflows.
Big thanks to @nextflow.io, @evanfloden.bsky.social, and @ewels.bsky.social for the support.
🎉 Together with @lukfor.bsky.social & @silvidm.bsky.social we'll work on improving imputation server workflows.
Big thanks to @nextflow.io, @evanfloden.bsky.social, and @ewels.bsky.social for the support.
January 29, 2025 at 10:56 AM
Looking forward to great discussions, learning, and sharing insights. Busy but productive days ahead!
Reposted by Lukas Forer
Yes, but can it run Doom?
`nextflow run doom`
✅ @nextflow.io (by @jordeu.bsky.social 🌟)
github.com/nextflow-io/...
`nextflow run doom`
✅ @nextflow.io (by @jordeu.bsky.social 🌟)
github.com/nextflow-io/...
January 22, 2025 at 8:11 AM
Yes, but can it run Doom?
`nextflow run doom`
✅ @nextflow.io (by @jordeu.bsky.social 🌟)
github.com/nextflow-io/...
`nextflow run doom`
✅ @nextflow.io (by @jordeu.bsky.social 🌟)
github.com/nextflow-io/...
Für die #Geoguessr Spieler unter uns: eine Map mit ca. 9.900 locations aus #Südtirol. Viel Spaß! 📍 www.geoguessr.com/maps/678e0b0...
GeoGuessr - Südtirol
Explore this map by lukfor on GeoGuessr
www.geoguessr.com
January 20, 2025 at 6:07 PM
Für die #Geoguessr Spieler unter uns: eine Map mit ca. 9.900 locations aus #Südtirol. Viel Spaß! 📍 www.geoguessr.com/maps/678e0b0...
Looking forward to spending two days working on the imputation server with fantastic people! Thanks to @seqera.io, @ewels.bsky.social and @chrishakk.bsky.social for sending us stickers 🙏
Are you working with one of the genotype imputation servers? Then this is your chance to see new features pretty soon on the server: @lukfor.bsky.social ky.social, @silvidm.bsky.social, and I are hosting our 2nd Nextflow in Genomics Hackathon to boost imputation servers here @i-med.ac.at
1/2
Nextflow In Genomics 2025 - Genepi Innsbruck
Institute of Genetic Epidemiology, Medical University of Innsbruck
genepi.i-med.ac.at
January 16, 2025 at 6:51 PM
Looking forward to spending two days working on the imputation server with fantastic people! Thanks to @seqera.io, @ewels.bsky.social and @chrishakk.bsky.social for sending us stickers 🙏
Reposted by Lukas Forer
For anyone who hasn’t already read the article, this is a pretty great video from Prime on it.
curiouscoding.nl/posts/static...
curiouscoding.nl/posts/static...
January 10, 2025 at 2:26 PM
For anyone who hasn’t already read the article, this is a pretty great video from Prime on it.
curiouscoding.nl/posts/static...
curiouscoding.nl/posts/static...
👏
Zeit, neue Wege zu gehen: Wir haben unsere Aktivitäten auf X beendet. Bleiben Sie mit uns im Dialog – hier bei Bluesky und auf unseren anderen Kanälen.
Mehr Info: https://www.i-med.ac.at/mypoint/thema/788987.html
#eXit #WissXit #ByeByeX #QuitX
Credit: HHU/Paul Schwaderer
Mehr Info: https://www.i-med.ac.at/mypoint/thema/788987.html
#eXit #WissXit #ByeByeX #QuitX
Credit: HHU/Paul Schwaderer
January 10, 2025 at 11:51 AM
👏
2024 is ending soon and it has been an exciting year for nf-test 🎉 A lot of new features and the amazing @nextflow.io community made nf-test even better 🚀 Thank you! 🙏
💡 What was your favorite nf-test update this year?
#Nextflow #Bioinformatics #recap
Here's a quick look back at 2024 🧵👇
💡 What was your favorite nf-test update this year?
#Nextflow #Bioinformatics #recap
Here's a quick look back at 2024 🧵👇
December 30, 2024 at 12:29 PM
2024 is ending soon and it has been an exciting year for nf-test 🎉 A lot of new features and the amazing @nextflow.io community made nf-test even better 🚀 Thank you! 🙏
💡 What was your favorite nf-test update this year?
#Nextflow #Bioinformatics #recap
Here's a quick look back at 2024 🧵👇
💡 What was your favorite nf-test update this year?
#Nextflow #Bioinformatics #recap
Here's a quick look back at 2024 🧵👇
Super cool! MultiQC now supports Haplocheck! 🚀 @sebschoenherr.bsky.social @whansi.bsky.social
🆕 10 new modules supporting new tools in this release:
- MosaiCatcher
- ataqv
- telseq
- Cell
- GTDB
- Checkm
- Checkm2
- Haplocheck
- mgikit
- Percolator
- MosaiCatcher
- ataqv
- telseq
- Cell
- GTDB
- Checkm
- Checkm2
- Haplocheck
- mgikit
- Percolator
December 22, 2024 at 11:29 AM
Super cool! MultiQC now supports Haplocheck! 🚀 @sebschoenherr.bsky.social @whansi.bsky.social
💻🧬
This summer, @lukfor.bsky.social and I migrated the Michigan Imputation Server to Nextflow. 2M genomes later, we can say it was a big success.
As a Christmas gift, we’re excited to show you how to set up your own local server in under 10 minutes.
##freeimputation
genepi.github.io/michigan-imp...
As a Christmas gift, we’re excited to show you how to set up your own local server in under 10 minutes.
##freeimputation
genepi.github.io/michigan-imp...
December 19, 2024 at 6:03 PM
💻🧬
Reposted by Lukas Forer
If you're looking to connect with other researchers and physicians in the cardiovascular field, join this Starter Pack. #CardioSky #MedSky #GeneSky #ImmunoSky
go.bsky.app/VEqq8ML
go.bsky.app/VEqq8ML
December 13, 2024 at 6:38 PM
If you're looking to connect with other researchers and physicians in the cardiovascular field, join this Starter Pack. #CardioSky #MedSky #GeneSky #ImmunoSky
go.bsky.app/VEqq8ML
go.bsky.app/VEqq8ML