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nf-co.re
nf-core
@nf-co.re
2K followers 14 following 390 posts
A community effort to collect a curated set of analysis pipelines built using Nextflow.
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nf-co.re
Pipeline release! nf-core/rnaseq v3.22.1 - nf-core/rnaseq v3.22.1 - Polished Palladium Penguin!

Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.22.1
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 ...
github.com
December 5, 2025 at 6:25 PM
nf-co.re
Pipeline release! nf-core/viralmetagenome v1.0.1 - 1.0.1 - Khaki Quail!

Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.0.1
Release 1.0.1 - Khaki Quail · nf-core/viralmetagenome
v1.0.1 - 2025-12-03 Added Update modules (#237) (by @Joon-Klaps) Fixed Template merge from nf-core/tools v3.5.1 (#236) (by @Joon-Klaps) Fix bug with numeric sample ids in custom_multiqc.py modul...
github.com
December 5, 2025 at 12:59 PM
nf-co.re
Pipeline release! nf-core/mag v5.3.0 - mag 5.3.0 - Rainbow Rattlesnake!

Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.3.0
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...
github.com
December 5, 2025 at 12:03 PM
nf-co.re
Pipeline release! nf-core/rnavar v1.2.2 - nf-core/rnavar 1.2.2 - Gray Red Tail!

Please see the changelog: https://github.com/nf-core/rnavar/releases/tag/1.2.2
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...
github.com
December 5, 2025 at 10:10 AM
nf-co.re
Pipeline release! nf-core/sarek v3.7.0 - 3.7.0 - Saltoluokta!

Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.7.0
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...
github.com
December 4, 2025 at 5:06 PM
nf-co.re
🧑‍💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?

We are merging the 🌍 Eur/M.E./Afr and the 🌎 Americas weekly helpdesk.

Please join our nf-core maintainers, this Thursday at 14:30 CET | 08:30 ET on play.workadventu.re/@/nf-core/nf...
December 3, 2025 at 5:35 PM
nf-co.re
Pipeline release! nf-core/variantbenchmarking v1.4.0 - Thin Yasar!

Please see the changelog: https://github.com/nf-core/variantbenchmarking/releases/tag/1.4.0
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 ...
github.com
December 3, 2025 at 3:23 PM
nf-co.re
Pipeline release! nf-core/riboseq v1.2.0 - nf-core/riboseq v1.2.0 - Mercury Spider!

Please see the changelog: https://github.com/nf-core/riboseq/releases/tag/1.2.0
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...
github.com
December 3, 2025 at 2:58 PM
Reposted by nf-core
nextflow.io
"Using open source tools like Nextflow and @nf-co.re allows organizations to run best practice pipelines off the shelf, which are reproducible and can be executed on various infrastructures.”

Check out ELIXIR's report on how open source software drives innovation in life sciences research. ⬇️
elixir-europe.org ELIXIR Europe @elixir-europe.org · 10d
Large, complex datasets 💾 are fundamental to the life sciences and form the backbone of innovation. 📣 ELIXIR has published a report on the contribution of #OpenSource #software and #workflows to innovation in the #lifesciences 🔬.

Read the news 👉 https://loom.ly/THB_IX4
December 2, 2025 at 8:27 AM
nf-co.re
Pipeline release! nf-core/phaseimpute v1.1.0 - 1.1.0 - Purple Beagle!

Please see the changelog: https://github.com/nf-core/phaseimpute/releases/tag/1.1.0
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...
github.com
December 1, 2025 at 6:33 PM
nf-co.re
Pipeline release! nf-core/magmap vv1.0.0 - magmap v1.0.0!

Please see the changelog: https://github.com/nf-core/magmap/releases/tag/v1.0.0
Release magmap v1.0.0 · nf-core/magmap
Contributors @danilodileo @emnilsson @erikrikarddaniel Full Changelog: https://github.com/nf-core/magmap/commits/release
github.com
November 28, 2025 at 4:12 PM
nf-co.re
Pipeline release! nf-core/rnaseq v3.22.0 - nf-core/rnaseq v3.22.0 - Palladium Penguin!

Please see the changelog: https://github.com/nf-core/rnaseq/releases/tag/3.22.0
Release nf-core/rnaseq v3.22.0 - Palladium Penguin · nf-core/rnaseq
What's Changed Bump after release 3.21.0 by @pinin4fjords in #1608 Important! Template update for nf-core/tools v3.4.1 by @nf-core-bot in #1614 Bbsplit staging issue by @EladH1 in #1617 Optimize q...
github.com
November 27, 2025 at 10:49 AM
nf-co.re
🧑‍💻 Need help with #nfcore #nextflow #bioinformatics pipelines, running or developing?

We are merging the 🌍 Eur/M.E./Afr and the 🌎 Americas weekly helpdesk.

Please join our host @vagkaratzas.bsky.social, nf-core maintainer, this Thursday at 14:30 CET | 08:30 ET on play.workadventu.re/@/nf-core/nf...
November 25, 2025 at 11:07 AM
nf-co.re
Pipeline release! nf-core/proteinfamilies v2.1.0 - Iron Goat!

Please see the changelog: https://github.com/nf-core/proteinfamilies/releases/tag/2.1.0
Release Iron Goat · nf-core/proteinfamilies
Added #133 - Using the new workflow output syntax to publish the downstream nf-core/proteinfold samplesheet. (by @vagkaratzas) #132 - Added optimized memory and time resources for test and test_fu...
github.com
November 25, 2025 at 10:48 AM
nf-co.re
Pipeline release! nf-core/taxprofiler v1.2.5 - v1.2.5 - Bouncy Basenji Patch!

Please see the changelog: https://github.com/nf-core/taxprofiler/releases/tag/1.2.5
Release v1.2.5 - Bouncy Basenji Patch · nf-core/taxprofiler
Added #640 Added support for saving Metaphlan SAM files (❤️ to @mr2raccoon for reporting and added by @jfy133) #657, #667 Template update for nf-core/tools v3.4.1 and v3.5.1 (added by @sofstam and...
github.com
November 21, 2025 at 3:08 PM
nf-co.re
Pipeline release! nf-core/epitopeprediction v3.1.0 - 3.1.0 - Lustnau!

Please see the changelog: https://github.com/nf-core/epitopeprediction/releases/tag/3.1.0
Release 3.1.0 - Lustnau · nf-core/epitopeprediction
3.1.0 - Lustnau - 2025-11-19 Added #304 Added --binder_only parameter to filter out non-binding peptides from the final results #306 Added nf-co2footprint plugin Fixed #290 Fixed an issue where ...
github.com
November 21, 2025 at 10:25 AM
nf-co.re
Pipeline release! nf-core/methylong v2.0.0 - 3!

Please see the changelog: https://github.com/nf-core/methylong/releases/tag/2.0.0
Release 3 · nf-core/methylong
github.com
November 21, 2025 at 2:26 AM
nf-co.re
New blog post! Topic: Topics
https://nf-co.re/blog/2025/version_topics/
November 19, 2025 at 4:02 PM
nf-co.re
New blog post! nf-core/tools - 3.5.0
https://nf-co.re/blog/2025/tools-3_5_0/
November 19, 2025 at 4:02 PM
nf-co.re
Pipeline release! nf-core/rnafusion v3.0.1b - 3.0.1b!

Please see the changelog: https://github.com/nf-core/rnafusion/releases/tag/3.0.1b
November 18, 2025 at 3:04 PM
nf-co.re
New blog post! The nf-core roadmap for adopting the new Nextflow syntax
https://nf-co.re/blog/2025/nextflow_syntax_nf-core_roadmap/
November 17, 2025 at 4:02 PM
Reposted by nf-core
nextflow.io
Welcome to the @nf-co.re Hackathon in Barcelona!🙌 All experience levels joining forces for collaborative pipeline development, community connection, and plenty of fun along the way. Let the coding and collaboration begin! #NextflowSummit
October 28, 2025 at 9:23 AM
Reposted by nf-core
science.ninja
So glad that a feature I've wanted, and then worked on, is finally out!

Run all the bin QC tools now!
November 7, 2025 at 8:29 PM
nf-co.re
Pipeline release! nf-core/detaxizer v1.3.0 - detaxizer 1.3.0 - rausgruschdla!

Please see the changelog: https://github.com/nf-core/detaxizer/releases/tag/1.3.0
Release detaxizer 1.3.0 - rausgruschdla · nf-core/detaxizer
Summary of changes Alternative filtering tool with --filtering_tool bbmap (default as previous versions with seqkit) Added peer-reviewed paper as pipeline citation Updated nf-core modules software...
github.com
November 14, 2025 at 11:41 AM
nf-co.re
Pipeline release! nf-core/createtaxdb v2.0.0 - v2.0.0 - Charming Chaac - [2025-11-14]!

Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/2.0.0
Release v2.0.0 - Charming Chaac - [2025-11-14] · nf-core/createtaxdb
Added #108 - Document workaround for building databases from single FASTA files, e.g. from NCBI RefSeq (by @pcantalupo) #111 - Added sourmash reference building both for genomes and proteomes (by ...
github.com
November 14, 2025 at 10:10 AM