nf-core
@nf-co.re
A community effort to collect a curated set of analysis pipelines built using Nextflow.
Pipeline release! nf-core/seqsubmit v1.0.0 - 1.0.0! Please see the changelog: https://github.com/nf-core/seqsubmit/releases/tag/1.0.0
Release 1.0.0 · nf-core/seqsubmit
Initial release of nf-core/seqsubmit Added The pipeline supports four submission modes via dedicated workflows: mags — Metagenome Assembled Genomes submission (GENOMESUBMIT) bins — Metagenomic bin...
github.com
Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03! Please see the changelog: https://github.com/nf-core/phyloplace/releases/tag/2.1.0
Release v2.1.0 - 2026-08-03 · nf-core/phyloplace
Added #63 - Report hmmbuild, EPA-NG and GAPPA heat tree logs/output in MultiQC (#3) (by @erikrikarddaniel) Changed #62 - Template update to 4.0.3 and software updates (by @erikrikarddaniel)
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Pipeline release! nf-core/mag v5.5.0 - mag 5.5.0 - Purple Penguin! Please see the changelog: https://github.com/nf-core/mag/releases/tag/5.5.0
Release mag 5.5.0 - Purple Penguin · nf-core/mag
Added #908 - Add nf-test snapshot for test_single_end profile (by @dialvarezs) #1028 - Add nf-test snapshot for test_longread_alternatives profile (by @dialvarezs) #1029 - Add nf-test snapshot for...
github.com
New blog post! nf-core/tools - 4.1.0 https://nf-co.re/blog/2026/tools-4_1_0/
Pipeline release! nf-core/pairgenomealign v3.0.3 - nf-core/pairgenomealign v3.0.3 – Kanten! Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/3.0.3
Release nf-core/pairgenomealign v3.0.3 – Kanten · nf-core/pairgenomealign
v3.0.3 "Kanten" - [July 29th 2026] Fixed Remove vulnerable PR-comment artifact pattern – no change in the pipeline computations (#145). Conforms to nf-core template version 4.0.3 (#144). In the fu...
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We're heading to Barcelona on Oct 15-16 for an in-person hackathon. Whether you're already involved in nf-core or not, this hackathon is the perfect place to get to know members of the @nextflow.io community.
📢 Deadline tomorrow: Speak at the #NextflowSummit by @seqera.io this Oct.🎤 We want to hear how you're using Nextflow to solve real bioinformatics challenges at scale, from pipeline development to agentic approaches and more. Submit your abstract now: hubs.la/Q04qsyFn0
Only ONE WEEK left to submit your talk abstract for the online #NextflowSummit in October! 📅🔥 Get those abstracts in quick! 😅
Nextflow@nextflow.io · 3w ago🎤 The #NextflowSummit returns on Oct 13-14, and we're looking for speakers to share their experience using Nextflow for scalable, reproducible analysis.🌎 Submit your talk abstract by July 24 to share your work with global community. 🔗 hubs.la/Q04pMYJ80
Pipeline release! nf-core/pixelator v5.0.0 - nf-core/pixelator 5.0.0! Please see the changelog: https://github.com/nf-core/pixelator/releases/tag/5.0.0
Release nf-core/pixelator 5.0.0 · nf-core/pixelator
[5.0.0] - 2026-07-13 Changed (breaking change) Rename pna_sample_calling_confidence_threshold to pna_sample_calling_enrichment_threshold to match pixelator 0.29.0. By @elhb #227 Change default lay...
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Pipeline release! nf-core/sopa v1.0.0 - v1.0.0 - [2026-07-15]! Please see the changelog: https://github.com/nf-core/sopa/releases/tag/1.0.0
Release v1.0.0 - [2026-07-15] · nf-core/sopa
Initial release of nf-core/sopa, created with the nf-core template.
github.com
New @nf-co.re monthly #newsletter is live! Read all about it in a new blog post out today: nf-co.re/blog/2026/ne... You can get monthly emails, or subscribe on LinkedIn: www.linkedin.com/newsletters/... Little promo clip made using hyperframes.heygen.com just for fun 😅
Nextflow Ambassadors play such an important role in the growth of the global community.🌎 Nextflow Ambassador Jimmy Lail (@northeasternu.bsky.social) shares his journey toward contributing his very first @nf-co.re pull request. 📚 Read the blog: hubs.la/Q04phxrZ0
From Confused to Contributing: My First nf-core PR Journey | Seqera
What I learned adding DIAMOND-blastp to proteinannotator and what I wish I'd known beforehand. If you're a bioinformatics student thinking about making your first nf-core contribution, this is the pos...
hubs.la
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 - 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 ...
github.com
Pipeline release! nf-core/seqinspector v1.1.0 - nf-core/seqinspector 1.1.0 - Veronica Mars! Please see the changelog: https://github.com/nf-core/seqinspector/releases/tag/1.1.0
Release nf-core/seqinspector 1.1.0 - Veronica Mars · nf-core/seqinspector
What's Changed Back to dev by @maxulysse in #191 FEAT: Refactor tools selection by @maxulysse in #192 Docs update by @FranBonath in #205 FEAT: add --fai option by @maxulysse in #202 Adds FASTQE fo...
github.com
Spaces are filling up for the nf-core Hackathon in Barcelona!👩💻 Early bird registration is 25% off until Jul 31. 📅 Oct 15-16, 2026 📍 Hotel SB Glow, Barcelona 🔗 summit.nextflow.io/2026/barcelo...
Pipeline release! nf-core/raredisease v3.1.2 - 3.1.2 - Princess Peach (patch)! Please see the changelog: https://github.com/nf-core/raredisease/releases/tag/3.1.2
Release 3.1.2 - Princess Peach (patch) · nf-core/raredisease
What's Changed add filter logic for mt snv merging by @ramprasadn in #915 fix the issue described in #909 Full Changelog: 3.1.1...3.1.2
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Join us on August 15-16 for HackNatal 2026, an nf-core Hackathon in Brazil, held as part of the SNNB.🌎 Bring your own topic or choose from open issues in the community. Each project has a lead who can guide you in the right direction: hubs.la/Q04nBcSd0
Hackathon - Agosto 2026
Um hackathon presencial para contribuir com tarefas do nf-core e de seus projetos Nextflow
hubs.la
Pipeline release! nf-core/scrnaseq v4.2.0 - 4.2.0! Please see the changelog: https://github.com/nf-core/scrnaseq/releases/tag/4.2.0
Release 4.2.0 · nf-core/scrnaseq
What's Changed Update to cellranger v10.0.0 by @tgelafr-pfzr in #508 Fix bug with probeset and index mismatch when using cellranger multi with a probeset and without a pre-built index by @tgelafr-...
github.com
Pipeline release! nf-core/createtaxdb v3.1.0 - v3.1.0 - Seductive Siren - [2026-07-03]! Please see the changelog: https://github.com/nf-core/createtaxdb/releases/tag/3.1.0
Release v3.1.0 - Seductive Siren - [2026-07-03] · nf-core/createtaxdb
Added #194 - Updated to nf-core template 4.0.2 (by @jfy133) #195 - Added Centrifuger database building support (by @haris18s) Fixed #196 - Improved KrakenUniq build clean up step (by @mahesh-pan...
github.com
Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0! Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0
Release 2.0.0 · nf-core/mcmicro
This release marks the point where the pipeline was moved from labsyspharm/mcmicro over to the new nf-core community, at nf-core/mcmicro. View the previous changelog at labsyspharm/mcmicro/CHANGES....
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Pipeline release! nf-core/viralmetagenome v1.1.3 - v1.1.3 - Cerulean Crane ! Please see the changelog: https://github.com/nf-core/viralmetagenome/releases/tag/1.1.3
Release v1.1.3 - Cerulean Crane · nf-core/viralmetagenome
v1.1.3 - 2026-07-02 Added Fixed default value of --reference_pool from current to C-RVDBv31.0 as RVDB changed their default link from fasta.gz to fasta.tar.gz which can no longer be directly integ...
github.com
Pipeline release! nf-core/mcmicro v2.0.0 - 2.0.0! Please see the changelog: https://github.com/nf-core/mcmicro/releases/tag/2.0.0
Release 2.0.0 · nf-core/mcmicro
This release marks the point where the pipeline was moved from labsyspharm/mcmicro over to the new nf-core community, at nf-core/mcmicro. View the previous changelog at labsyspharm/mcmicro/CHANGES....
github.com
New blog post! Maintainers Minutes: May - June 2026 https://nf-co.re/blog/2026/maintainers-minutes-2026-06-26/
Pipeline release! nf-core/sarek v3.9.0 - 3.9.0 - Sarvesjåhkå! Please see the changelog: https://github.com/nf-core/sarek/releases/tag/3.9.0
Release 3.9.0 - Sarvesjåhkå · nf-core/sarek
What's Changed Back to dev (3.9.0dev) by @FriederikeHanssen in #2139 fix: sort final vcf in varlociraptor sbwfs and update varlociraptor by @famosab in #2055 Add CRAM_TO_BAM to parabricks by @famo...
github.com
Pipeline release! nf-core/pairgenomealign v3.0.1 - nf-core/pairgenomealign v3.0.1 – Tokoroten! Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/3.0.1
Release nf-core/pairgenomealign v3.0.1 – Tokoroten · nf-core/pairgenomealign
v3.0.1 "Tokoroten" - [June 29th 2026] Fixed Fix strict syntax error when using --multi-cram. Run the long test with the RY4 seed and --multi-cram as a better showcase.
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Pipeline release! nf-core/rnadnavar v1.0.0 - 1.0.0 - restless hermit! Please see the changelog: https://github.com/nf-core/rnadnavar/releases/tag/1.0.0
Release 1.0.0 - restless hermit · nf-core/rnadnavar
nf-core/rnadnavar v1.0.0 The first release of nf-core/rnadnavar is (finally!) here 🚀. v1.0.0 delivers a full workflow for somatic variant discovery and refinement from DNA and RNA data, covering va...
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Pipeline release! nf-core/funcscan v4.0.0 - v4.0.0 - Chinese Baozi - 2026-06-27! Please see the changelog: https://github.com/nf-core/funcscan/releases/tag/4.0.0
Release v4.0.0 - Chinese Baozi - 2026-06-27 · nf-core/funcscan
v4.0.0 - Chinese Baozi - [2026-06-27] Breaking change #530 Updated AMPcombi, changed parameter amp_ampcombi_cluster_removesingletons into amp_ampcombi_cluster_keepsingletons. (by @jasmezz, @jfy13...
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Pipeline release! nf-core/scnanoseq v1.3.0 - nf-core/scnanoseq v1.3.0 - Steel Elephant! Please see the changelog: https://github.com/nf-core/scnanoseq/releases/tag/1.3.0
Release nf-core/scnanoseq v1.3.0 - Steel Elephant · nf-core/scnanoseq
v1.3.0 [2026-06-26] Credits Special thanks to a new contributor to scnanoseq: Nick Youngblut Enhancements #94 Strict syntax conversion: converted entire workflow to strict syntax and reorganized...
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Pipeline release! nf-core/longraredisease v1.0.0 - 1.0.0! Please see the changelog: https://github.com/nf-core/longraredisease/releases/tag/1.0.0
Release 1.0.0 · nf-core/longraredisease
Initial release of nf-core/longraredisease, created with the nf-core template. This release provides an end-to-end pipeline for comprehensive variant detection: structural variants (SV), single-nuc...
github.com
Pipeline release! nf-core/pairgenomealign v3.0.0 - nf-core/pairgenomealign v3.0.0 – Tokoroten! Please see the changelog: https://github.com/nf-core/pairgenomealign/releases/tag/3.0.0
Release nf-core/pairgenomealign v3.0.0 – Tokoroten · nf-core/pairgenomealign
v3.0.0 "Tokoroten" - [June 26th 2026] Breaking changes Simplify output file names by removing _aln and _plt. Update all modules to latest versions. Use the default CRAM format from samtools (CRAM ...
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