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Maxime U Garcia

@maxulysse.github.io
1.6K followers 1.5K following 26 posts

Bioinfomagician/PhD in Bioinformatics, developing @nextflow.io @nf-co.re pipelines Posts and RPs in English/French - He/him

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Reposted by Maxime U Garcia
nf-core @nf-co.re · 23/09/2026
The Barcelona nf-core Hackathon is happening in 3 weeks!⏳ Choose from 13 projects to work on, or bring your own project idea. Today's project spotlight 👇 ⚒️ Project → Benchmarking (Special Interest Group) 🧑‍💻 Project Lead → Kübra Narci, @ghga.bsky.social 🔗 Project Link → nf-co.re/hackathon-pr...
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nf-core @nf-co.re · 25/09/2026
📆 We've extended the deadline for the Barcelona Hackathon! Choose from 13 hackathon projects, or bring your own project idea.💡Today's project spotlight ⬇️ ⚒️ Project → AWS megatests overhaul 🧑‍💻 Project Lead → @rikehanssen.bsky.social, @seqera.io 🔗 Project Link → hubs.la/Q04yjbwG0
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nf-core @nf-co.re · 24/09/2026
We have now have 13 projects for the Barcelona Hackathon.⛰️Check out today's project spotlight 👇 #NextflowSummit ⚒️ Project → nf-core/sarek improvements 🧑‍💻 Project Lead → @maxulysse.github.io, @scilifelab-ngi.bsky.social 🔗 Project Link → nf-co.re/hackathon-pr...
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Nextflow @nextflow.io · 21/09/2026
Saba Nafees (Myriad Genetics)→ From production Nextflow to cross-pipeline MRD variant calling via @nf-co.re /sarek summit.nextflow.io/2026/virtual...
summit.nextflow.io
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Nextflow @nextflow.io · 07/09/2026
🌎Whether you're joining the online #NextflowSummit or heading to Barcelona for the @nf-co.re Hackathon or Nextflow Training, let us know you're attending!👾 Register now to create your pixel avatar: hubs.la/Q04wQpTZ0
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Stephen Turner @stephenturner.us · 21/08/2026
I spent most of my time at the 2024 #Nextflow @nf-co.re hackathon working on genomeqc. Happy to see our preprint finally published: nf-core/genomeqc: a best-practice pipeline for comparing genome and assembly quality: www.biorxiv.org/content/10.6... 🧬💻🧪 github.com/nf-core/geno...
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Nextflow @nextflow.io · 31/07/2026
⏰ If you're looking to join us in Barcelona for Nextflow Training or the @nf-co.re Hackathon on October 15-16, today is your last chance to save 25%: hubs.la/Q04rsgWS0 #NextflowSummit
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Seqera @seqera.io · 24/07/2026
What's Happening? 🔹 Beginners Training - Learn how to build and run multi-step Nextflow workflows 🔹 Advanced Training - Explore advanced Nextflow capabilities to help you develop 🔹 @nf-co.re Hackathon - Collaborate on projects with the Nextflow community
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Seqera @seqera.io · 24/07/2026
Join us in Barcelona on Oct 15-16 for @nextflow.io Training or the @nf-co.re Hackathon at the #NextflowSummit 2026!👩‍💻Register by Jul 31 for 25% off: hubs.la/Q04qFpbC0
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Maxime U Garcia @maxulysse.github.io · 15/07/2026
Any other suggestions @nanojess.io ?
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Maxime U Garcia @maxulysse.github.io · 15/07/2026
Here you go: github.com/nf-core/seqi...
github.com
Add chelae/trim as an alternate trimming tool by maxulysse · Pull Request #260 · nf-core/seqinspector
Add chelae/trim from nf-core/modules as an alternative to fastp for adapter trimming and quality filtering of short-read FASTQ data. Changes Installed nf-core/chelae/trim module with patch for mul...
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Maxime U Garcia @maxulysse.github.io · 14/07/2026
Any other tools you would want to see in such a pipeline? What do you usually put in?
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Reposted by Maxime U Garcia
Jess Smith @nanojess.io · 14/07/2026
I cannot tell you how many times I've written basically this QC pipeline. Countless! Uncountable! Glad to see this addition to @nf-co.re. Also, @tfenne.bsky.social, is this the first nf-core pipeline with Riker support? Or did I miss one? github.com/nf-core/seqi...
github.com
GitHub - nf-core/seqinspector: Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The...
Dedicated QC-only pipeline for sequencing data. The pipeline will run a (potentially large) set of QC tools and can output global and group specific Multiqc reports. The pipeline is targeting core ...
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Reposted by Maxime U Garcia
nf-core @nf-co.re · 23/06/2026
Happening right now: join @ewels.bsky.social in a @nf-co.re #bytesize talk to hear all about our newest feature: monthly Newsletters! nf-co.re/events/2026/...
nf-co.re
Bytesize: nf-core newsletter
Phil Ewels, Seqera
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Seqera @seqera.io · 17/06/2026
Interested in learning @nextflow.io?🌟Explore our upcoming Nextflow events and training opportunities below🧵 💻 What: Webinar - What's New in Nextflow 26.04 📅 When: TODAY 📍 Where: Online seqera.io/events/what-...
seqera.io
What's New in Nextflow 26.04: Strict Syntax, Records, Static Typing & the Module Registry | Seqera
At the Nextflow Summit Boston, we announced the release of Nextflow 26.04, with new capabilities to help you write bug-free pipeline code and catch errors early. We also introduced the Nextflow Module...
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Samuel Lampa @smllmp.bsky.social · 23/05/2026
TaxProfiler, the @nf-co.re #metagenomics pipeline had a new major release, adding multiple cool new classifiers (metacache, sylph and melon)! Great work by Sofia, @lilianderssonli.bsky.social , @jfy133.genomic.social.ap.brid.gy and others! 🙌 github.com/nf-core/taxp...
github.com
Release v2.0.0 - Crazy Corgi · nf-core/taxprofiler
Added #682 Added metacache classifier and improved nf-tests (added by @sofstam) #559 Profiling of long reads with motus (added by @LilyAnderssonLee and @sofstam ) #591 Add options to enable the ab...
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Australian BioCommons @ausbiocommons.bsky.social · 11/05/2026
Final call for our nf-core workshop! ⏳🧬 Applications close this Wednesday, 13 May. Don't miss your chance to master workflow customisation for @nf-co.re pipelines with our expert trainers. Apply here: www.biocommons.org.au/events/nf-co... @sydney-crf.bsky.social
biocommons.org.au
WORKSHOP: Unlocking nf-core: customising workflows for your research — Australian BioCommons
A practical workshop to set you up with the foundational knowledge required to run and customise nf-core workflows in a reproducible manner. More information Apply
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Nextflow @nextflow.io · 05/05/2026
Self-paced Online Nextflow Training from the Nextflow Creators!🎓 Join @seqera.io on May 11-15 for Nextflow Training Week. Whether you're completely new to workflow management or ready to advance your skills, there's something for you. 🔗 Register now: hubs.la/Q04fnXdz0
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Nextflow @nextflow.io · 28/04/2026
Who doesn't love swag?🔥 Check out the latest from the #NextflowSummit. @nextflow.io, @seqera.io, and @nf-co.re goodies - stickers and socks from the nf-core hackathon and training here in Boston!
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Phil Ewels @ewels.bsky.social · 02/04/2026
Super excited to be launching two things today: #RustQC 🦀🧬 and rewrites.bio 🚀 I used AI to rewrite 15 RNA-seq QC tools into a single Rust binary (I've never written any Rust). It ended up being over 60x faster. Here's the story 🧵 seqeralabs.github.io/RustQC/
seqeralabs.github.io
Welcome to RustQC
Fast quality control tools for sequencing data, written in Rust.
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Nextflow @nextflow.io · 16/03/2026
We're thrilled to welcome 46 new Nextflow Ambassadors in 2026!🌍 This milestone brings our global community to a remarkable 143 ambassadors across 40 countries (our largest cohort ever).🎉 Here's to building the future of scientific workflows together! 🚀
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Nextflow @nextflow.io · 20/01/2026
Nextflow Ambassador Nour Mahfel shares her journey from complete beginner to @nf-co.re contributor with support from @seqera.io. Learn how she shifted her mindset to think in dataflow, upstream modules, and embrace working in the open.📚 hubs.la/Q03_gcw_0
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nf-core @nf-co.re · 17/01/2026
New blog post! Running nf-core pipelines on ARM nf-co.re/blog/2026/arm-pipelines
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Maxime U Garcia @maxulysse.github.io · 16/01/2026
You are of course welcome to join us on Slack: nf-co.re/join cf nfcore.slack.com/archives/CE8...
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Maxime U Garcia @maxulysse.github.io · 16/01/2026
- Remove all GTF entries without proper strand (this is especially appropriate if those entries are not meant to denote proper exons or transcripts anyway, but something else).
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Maxime U Garcia @maxulysse.github.io · 16/01/2026
- Find a better GTF. (Have a look at Ensembl; I have a GTF from release 108 lying around which only has + or - in the strand column.) - Find out what the strand should be and replace the ? with the appropriate symbol.
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Maxime U Garcia @maxulysse.github.io · 16/01/2026
From a community member on Slack: Transcripts are inherently stranded, so ? as strand does not make sense, and any tool has no choice but to refuse to deal with this. Work-arounds (in order of preference):
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Mirko Pegoraro PhD @3volution.bsky.social · 15/01/2026
Today I figured how to use Nextflow to analyse my RNA seq data: very happy. @nf-co.re
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JOBIM 2026 @jobim2026.bsky.social · 13/01/2026
Les organisateurs des #JOBIM2026 vous souhaitent une ✨ bonne année 2026 ✨ ! 📣 Rappel : l’appel à mini-symposia est ouvert ✅ 🚨 Il vous reste 8 jours pour soumettre vos propositions ! 📅 Deadline : 21 janvier ! 🔗 Infos & modalités : premc.org/jobim-2026/ #JOBIM2026 #bioinfo #symposium #Strasbourg
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nf-core @nf-co.re · 14/01/2026
New blog post! nf-core and AI nf-co.re/blog/2026/statement-on-ai
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Nextflow @nextflow.io · 07/01/2026
Kickstart 2026 with all the latest features of Nextflow, including static types & workflow inputs/outputs!🚀 Watch the latest @seqera.io webinar showcasing these capabilities using @nf-co.re /RNAseq! 👀 Watch on-demand: hubs.la/Q03ZRYYg0
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Maxime U Garcia @maxulysse.github.io · 19/12/2025
On a server bright on Christmas night, MultiQC sang, “All stats unite!” From FastQC, pipelines adored, One tidy report—what could you want more?
First line Multiqc CLI output, saying MultiQC, followed by a Xmas tree emoji and version 1.31
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nf-core @nf-co.re · 01/12/2025
Pipeline release! nf-core/phaseimpute v1.1.0 - 1.1.0 - Purple Beagle! Please see the changelog: github.com/nf-core/phaseimpute/rele…
github.com
Release 1.1.0 - Purple Beagle · nf-core/phaseimpute
What's Changed This release adds two new imputation tools: Beagle5 and Minimac4. It also updates the templates to match the latest version of nf-core (v3.5.1). Special thanks to Kübra Narci and Die...
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nf-core @nf-co.re · 03/12/2025
Pipeline release! nf-core/riboseq v1.2.0 - nf-core/riboseq v1.2.0 - Mercury Spider! Please see the changelog: github.com/nf-core/riboseq/releases…
github.com
Release nf-core/riboseq v1.2.0 - Mercury Spider · nf-core/riboseq
What's Changed Json schema improvements by @andreirie in #103 Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in #111 Feat ribowaltz by @iraiosub in #113 Feat tubemap by @iraio...
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nf-core @nf-co.re · 03/12/2025
Pipeline release! nf-core/variantbenchmarking v1.4.0 - Thin Yasar! Please see the changelog: github.com/nf-core/variantbenchmark…
github.com
Release Thin Yasar · nf-core/variantbenchmarking
What's Changed Pipeline Release 1.4.0 by @kubranarci in #253 New functions Adding concordance analysis for query samples by @kubranarci in #237 239 add happy sompy and truvari in multiqc report ...
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nf-core @nf-co.re · 04/12/2025
Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta! Please see the changelog: github.com/nf-core/sarek/releases/t…
github.com
Release 3.7.0 - Saltoluokta · nf-core/sarek
What's Changed New Tools #2044 - Added VCF filtering with bcftools after variant calling #2049 - Added consensus calling for small variants called by multiple tools (default: 2+ tools) New Parame...
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nf-core @nf-co.re · 05/12/2025
Pipeline release! nf-core/rnavar v1.2.2 - nf-core/rnavar 1.2.2 - Gray Red Tail! Please see the changelog: github.com/nf-core/rnavar/releases/…
github.com
Release nf-core/rnavar 1.2.2 - Gray Red Tail · nf-core/rnavar
What's Changed use nf-core-utils by @maxulysse in #233 Important! Template update for nf-core/tools v3.4.0 by @nf-core-bot in #242 Important! Template update for nf-core/tools v3.4.1 by @nf-core-b...
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nf-core @nf-co.re · 05/12/2025
Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake! Please see the changelog: github.com/nf-core/mag/releases/tag…
github.com
Release mag 5.3.0 - Rainbow Rattlesnake · nf-core/mag
Added #905 - Add nf-test snapshot for test_assembly_input profile (by @dialvarezs) #930 - Add binner SemiBin2 (by @d4straub) #861 - Added --generate_bigmag_file to execute the bigmag workflow that...
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nf-core @nf-co.re · 05/12/2025
Pipeline release! nf-core/rnaseq v3.22.1 - nf-core/rnaseq v3.22.1 - Polished Palladium Penguin! Please see the changelog: github.com/nf-core/rnaseq/releases/…
github.com
Release nf-core/rnaseq v3.22.1 - Polished Palladium Penguin · nf-core/rnaseq
What's Changed Bump after release 3.22.0 by @pinin4fjords in #1640 add ARM CI test by @mashehu in #1641 Long merge rsem by @EladH1 in #1642 Fix HISAT2 issues: BAM CSI index with UMI deduplication ...
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Nextflow @nextflow.io · 11/09/2025
The Nextflow training sessions are in full swing here in the UK, complete with all our favorite Nextflow, @nf-co.re, and @seqera.io swag! 🎉
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Phil Ewels @ewels.bsky.social · 01/09/2025
Here's a little easter egg for those of you using @seqera.io #platform.. 🥚 ✨ Recently we released a new feature that lets you set custom pipeline icons. What's less well known is that animated icons are also supported - party time!! 🪩 🥳 🎉 The trick is to rename your .gif to a .png file extension 🤫
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Phil Ewels @ewels.bsky.social · 27/08/2025
That feeling when AI can create cat videos with better @nextflow.io training content than you've made in years.. 😻 😹 Could this be the new face of #Nextflow at @seqera.io ?!
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Seqera @seqera.io · 05/08/2025
🎉Celebrating 10 Years of @multiqc.info What began as a simple QC reporting tool has evolved into an essential resource used by thousands worldwide, becoming integral to the #bioinformatics ecosystm. 🔍 Discover MultiQC: hubs.la/Q03Bh0wM0
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MultiQC @multiqc.info · 04/08/2025
🎉 Today marks 10 years since the very first @multiqc.info commit! What started as a simple tool for QC reports has grown into something used by thousands of labs worldwide. It's become a foundational tool in the fabric of #bioinformatics and it's a joy to see it play a small part in global research
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terradue @terradue.bsky.social · 20/06/2025
Next week, we'll be present at the @esaearth.esa.int Living Planet Symposium 2025 #LPS25, in Vienna, Austria. 🌍We’re thrilled to be part of the dialogue shaping the future of EO science and technology. www.linkedin.com/posts/terrad...
linkedin.com
Next week, Terradue will be present at the ESA Living Planet Symposium 2025, held in Vienna, Austria. | terradue
Next week, Terradue will be present at the ESA Living Planet Symposium 2025, held in Vienna, Austria. LPS is one of the most important global events dedicated to Earth Observation. We’re thrilled to b...
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Earth Observation Lab @humboldteolab.bsky.social · 26/06/2025
Coming up next at #LPS25: Felix Kummer et al.: Standardizing Earth Observation Workflows with Nextflow and nf-core 
 📍11:30 at Hall L3 @kelewinska.bsky.social @hostertp.bsky.social
Announcement for upcoming Earth Observation Lab contribution at living planet symposium 2025: 
Kummer et al.: Standardizing Earth Observation Workflows with Nextflow and nf-core
Session: D.04.02 Best practices for execution of algorithms and workflows across federated cloud environments
Where: Hall L3
When: Thursday 26.06.25 / 11:30 h
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Maxime U Garcia @maxulysse.github.io · 25/06/2025
I just helped assemble a tile for the LEGO Sentinel-2 Mosaic #LPS25 #ESA #EO
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Nextflow @nextflow.io · 29/05/2025
🎤 Did you catch Esha Joshi's talk on scaling with @seqera.io? In this talk, she shared how Seqera empowers scientists to scale code, compute, projects, and teams—from early experimentation to enterprise-level deployments. 💻 🔗 Watch the full talk here: hubs.la/Q03pHjL00
youtube.com
Esha Joshi: Scale with Seqera: Accelerate, Expand, and Collaborate
YouTube video by Nextflow
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nf-core @nf-co.re · 23/05/2025
Pipeline release! nf-core/bamtofastq v2.2.0 - 2.2.0 - Kathleen Booth! Please see the changelog: github.com/nf-core/bamtofastq/relea…
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Nextflow @nextflow.io · 20/05/2025
🎉 Nextflow Summit Boston 2025 – What a Week! Last week, we brought together industry experts from around the world to shape the future of biotech and pharma through innovation in data science and computational biology. Here are a some key highlights 🧵
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