nf-core @nf-co.re · 16h15 days to go until the Hackathon in Barcelona.⏳ Join us: hubs.la/Q04yHBpQ0 💡Choose from 1 of 14 hackathon projects or submit your own project idea! Today's project spotlight 🧵 102
nf-core @nf-co.re · 29/09/2026Pipeline release! nf-core/hadge v1.0.0 - v1.0.0 - [2026-08-23]! Please see the changelog: github.com/nf-core/hadge/releases/t…github.comRelease v1.0.0 - [2026-08-23] · nf-core/hadgeFirst stable release of nf-core/hadge, combining 11 hashing- and genotype-based deconvolution methods (vireo, demuxlet, freemuxlet, souporcell, htodemux, multiseq, bff, demuxem, gmm-demux, hasheddr... 000
nf-core @nf-co.re · 29/09/2026⏳ 16 days to go! Join the Barcelona Hackathon at the #NextflowSummit: hubs.la/Q04yxZJW0 Today's project spotlight ⬇️ ⚒️ Project → nf-core/seqinspector improvements 🧑💻 Project Lead → Franziska Bonath, @kthlibrary.bsky.social 🔗 Project Link → hubs.la/Q04yxZPT0 100
nf-core @nf-co.re · 28/09/2026⏳ 17 days until the Barcelona nf-core Hackathon! Join one of the existing projects, or bring your own! Today's project spotlight ⬇️ ⚒️ Project → nf-core/spatialaxe improvements 🧑💻 Project Lead → Florian Heyl, @cnag-eu.bsky.social 🔗 Project Link → hubs.la/Q04ypPWK0 110
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 112
nf-core @nf-co.re · 24/09/2026We 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... 111
nf-core @nf-co.re · 23/09/2026Pipeline release! nf-core/isoseq v3.0.1 - v3.0.1 - Mended Zooble! Please see the changelog: github.com/nf-core/isoseq/releases/…github.comRelease v3.0.1 - Mended Zooble · nf-core/isoseqWarningThis 3.0.0 major release have breaking changes. Samplesheets and command lines written for v2.0.0 will not work unmodified. See the v3.0.0 changelog notes for details. Patch release fixing ... 010
nf-core @nf-co.re · 23/09/2026Pipeline release! nf-core/rnaseq v3.27.0 - nf-core/rnaseq v3.27.0 - Vanadium Vulture! Please see the changelog: github.com/nf-core/rnaseq/releases/…github.comRelease nf-core/rnaseq v3.27.0 - Vanadium Vulture · nf-core/rnaseqA big release with new user-facing options, several bug fixes for edge cases (Azure, NCBI GTFs, kallisto-only runs, UMI-deduplicated BAMs), and two nf-core template updates. New features Screen co... 000
nf-core @nf-co.re · 23/09/2026Last chance to register for the Barcelona #NextflowSummit @nf-co.re #hackathon !! 🇪🇸 👩🏻💻 💫static.klipy.comTed Lasso Coach Beard Shouts 'Let's Go!'Alt: Ted Lasso Coach Beard Shouts 'Let's Go!' 001
nf-core @nf-co.re · 23/09/2026The 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... 136
nf-core @nf-co.re · 23/09/2026Pipeline release! nf-core/phyloplace v2.3.0 - v2.3.0 - 2026-09-23! Please see the changelog: github.com/nf-core/phyloplace/relea…github.comRelease v2.3.0 - 2026-09-23 · nf-core/phyloplaceAdded #95 - Accept gzipped input files throughout the pipeline, for every samplesheet column and individual file parameter alike (#76) (by @erikrikarddaniel) Changed #95 - Check the file name ex... 000
nf-core @nf-co.re · 22/09/202623 days to go until the Hackathon in Barcelona ⬇️ Check our today's project spotlight. ⚒️ Project → nf-core/mag improvements 🧑💻 Project Lead → Jonathan Rondeau-Leclaire, Université de Sherbrooke 🔗 Project Link → nf-co.re/hackathon-pr... 102
nf-core @nf-co.re · 22/09/2026Pipeline release! nf-core/stableexpression vv1.0.0 - nf-core/stableexpression v1.0.0 - Prunus persica! Please see the changelog: github.com/nf-core/stableexpression…github.comRelease nf-core/stableexpression v1.0.0 - Prunus persica · nf-core/stableexpressionInitial release of the nf-core/stableexpression pipeline. The full commit history is available here. 010
nf-core @nf-co.re · 22/09/2026Pipeline release! nf-core/isoseq v3.0.0 - v3.0.0 - Patchwork Zooble [21/09/2026]! Please see the changelog: github.com/nf-core/isoseq/releases/…github.comRelease v3.0.0 - Patchwork Zooble [21/09/2026] · nf-core/isoseqWarningThis is a major release with breaking changes. Samplesheets and command lines written for v2.0.0 will not work unmodified. See the migration notes below. Added New samplesheet-driven input... 000
nf-core @nf-co.re · 21/09/2026Pipeline release! nf-core/funcprofiler v1.0.0 - funcprofiler version 1.0.0! Please see the changelog: github.com/nf-core/funcprofiler/rel…github.comRelease funcprofiler version 1.0.0 · nf-core/funcprofilerInitial release! funcprofiler can handle single or paired-end short read data, and can run the following tools: HUMANnN RGI mifaser fmh-funprofiler 020
nf-core @nf-co.re · 21/09/2026We now have 12 projects for the Barcelona Hackathon on Oct 15-16! Today's project spotlight ⬇️ ⚒️ Project → Agentic module development 🧑💻 Project Lead → Evangelos Karatzas, @ebi.embl.org 🔗 Project Link → nf-co.re/hackathon-pr... 111
nf-core @nf-co.re · 18/09/2026Pipeline release! nf-core/genomeassembler v2.0.0 - 2.0.0 - Saffron Vulture! Please see the changelog: github.com/nf-core/genomeassembler/…github.comRelease 2.0.0 - Saffron Vulture · nf-core/genomeassembler2.0.0 - 'Saffron Vulture' - [2026-09-18] This is a major release, with breaking changes. The pipeline now implements topics to collect software version, the minimum nextflow version is 25.10.4. v2.... 022
nf-core @nf-co.re · 16/09/2026Pipeline release! nf-core/viralmetagenome v1.2.0 - v1.2.0 - Damson Dove! Please see the changelog: github.com/nf-core/viralmetagenome/…github.comRelease v1.2.0 - Damson Dove · nf-core/viralmetagenomev1.2.0 - 2026-09-16 Added (#312) - Fix #282 - drop unmapped reads from the contig-coverage alignment and unmapped read pairs from the alignments used in polishing and consensus refinement, and add... 000
nf-core @nf-co.re · 16/09/2026Pipeline release! nf-core/genomeqc v1.0.1 - 1.0.1 - Gray Fox! Please see the changelog: github.com/nf-core/genomeqc/release…github.comRelease 1.0.1 - Gray Fox · nf-core/genomeqcFixed Fixed ORTHO_SEQ_COUNT reading Orthogroups.tsv via a manually-built path into OrthoFinder's output directory, which is unsafe on cloud storage. It now uses OrthoFinder's emited channel orthog... 010
nf-core @nf-co.re · 15/09/2026Pipeline release! nf-core/riboseq v2.0.0 - nf-core/riboseq v2.0.0 - Nimble Narwhal! Please see the changelog: github.com/nf-core/riboseq/releases…github.comRelease nf-core/riboseq v2.0.0 - Nimble Narwhal · nf-core/riboseqnf-core/riboseq v2.0.0 - Nimble Narwhal This is a major release. nf-core/riboseq grows from a single-caller ORF-detection pipeline into a full cross-caller ORF discovery and quantification suite, w... 000
nf-core @nf-co.re · 15/09/2026Pipeline release! nf-core/demultiplex v1.8.0 - 1.8.0! Please see the changelog: github.com/nf-core/demultiplex/rele…github.comRelease 1.8.0 · nf-core/demultiplexWhat's Changed Add AGENTS.md file with nf-core agent instructions by @maxulysse in #398 Back to dev by @maxulysse in #399 Add volume=40gb to nf-test runners by @maxulysse in #401 Important! Templa... 000
nf-core @nf-co.re · 15/09/2026Pipeline release! nf-core/metatdenovo v1.4.1 - BBNorm Singularity/Apptainer TMPDIR fix! Please see the changelog: github.com/nf-core/metatdenovo/rele…github.comRelease BBNorm Singularity/Apptainer TMPDIR fix · nf-core/metatdenovoThis patch release fixes BBNorm failing under Singularity/Apptainer when the host's $TMPDIR isn't bind-mounted into the container -- surfaced as a misleading Cannot run program "bgzip" error even t... 000
Reposted by nf-coreNextflow @nextflow.io · 15/09/2026Just 1 month to go until Nextflow Training and @nf-co.re Hackathon in Barcelona!🧦 Here's a sneak peak at exclusive swag you'll receive: stickers, t'shirts, socks and more! Register by Sep 24 to join the fun: hubs.la/Q04xwzJB0 #NextflowSummit 113
nf-core @nf-co.re · 15/09/2026Pipeline release! nf-core/fetchngs v1.13.0 - nf-core/fetchngs v1-13.0 - Palladium Penguin ! Please see the changelog: github.com/nf-core/fetchngs/release…github.comRelease nf-core/fetchngs v1-13.0 - Palladium Penguin · nf-core/fetchngsWhat's Changed New pipeline support fetchngs now generates samplesheets for ampliseq, mag, metatdenovo, and sarek, alongside the existing atcseq, rnaseq, taxprofiler, and viralrecon support. fastq-... 020
nf-core @nf-co.re · 11/09/2026Pipeline release! nf-core/pixelator v5.0.2 - nf-core/pixelator 5.0.2! Please see the changelog: github.com/nf-core/pixelator/releas…github.comRelease nf-core/pixelator 5.0.2 · nf-core/pixelator[5.0.2] - 2026-09-11 Patches Enhancements & fixes Pass the collated software versions to the experiment summary report. By @Aratz #248 Restrict the all_results_for_reports topic to *.report.json, ... 010
nf-core @nf-co.re · 11/09/2026Pipeline release! nf-core/phyloplace v2.2.0 - v2.2.0 - 2026-09-11! Please see the changelog: github.com/nf-core/phyloplace/relea…github.comRelease v2.2.0 - 2026-09-11 · nf-core/phyloplaceAdded #79 - New optional reftreename sample sheet column, grouping rows that place onto the same reference tree so that the group is also grafted, classified and heat-treed as a whole, instead of ... 001
nf-core @nf-co.re · 10/09/2026Just 14 days left to register for the Barcelona Hackathon this October! We have so many great projects lined up already across pipelines, components, special interest groups, tooling, and community.🌍 Or bring your own ideas! 🔗 Register now: hubs.la/Q04x6Dw30 001
nf-core @nf-co.re · 08/09/2026Pipeline release! nf-core/rnastructurome v1.0.0 - 1.0.0! Please see the changelog: github.com/nf-core/rnastructurome/r…github.comRelease 1.0.0 · nf-core/rnastructuromeFirst release of nf-core/rnastructurome, which analyses chemical high-throughput RNA structure-probing data and predicts RNA secondary structures from it. The pipeline covers SHAPE and DMS chemistr... 010
nf-core @nf-co.re · 08/09/2026Join us in Barcelona on Oct 15-16! Register by Sep 24 to avoid missing out: hubs.la/Q04wTW1v0 012
nf-core @nf-co.re · 01/09/2026Pipeline release! nf-core/genomeqc v1.0.0 - 1.0.0! Please see the changelog: github.com/nf-core/genomeqc/release…github.comRelease 1.0.0 · nf-core/genomeqcFirst release of nf-core/genomeqc, which compares the quality of multiple genomes and their annotations. The pipeline runs in two modes depending on the inputs provided: Genome only (FASTA files) a... 010
nf-core @nf-co.re · 01/09/2026Pipeline release! nf-core/oncoanalyser v3.0.0 - 3.0.0 - Scarlet Honeyeater! Please see the changelog: github.com/nf-core/oncoanalyser/rel…github.comRelease 3.0.0 - Scarlet Honeyeater · nf-core/oncoanalyserWhat's Changed Post release bump by @scwatts in #273 Feat/hmf reference download by @rhassaine in #264 Remove vulnerable PR-comment artifact pattern by @scwatts in #308 #309 Apply Hartwig updates,... 000
nf-core @nf-co.re · 31/08/2026Pipeline release! nf-core/fastqrepair v1.1.1 - v1.1.1 - Reggina Amaranth [27/08/2026]! Please see the changelog: github.com/nf-core/fastqrepair/rele…github.comRelease v1.1.1 - Reggina Amaranth [27/08/2026] · nf-core/fastqrepairWhat's Changed [PR #32] - Template update for nf-core/tools v4.0.3 (supersedes the pending v3.4.1, v3.5.1 and v4.0.2 template merges). Issue #17 - Improved nextflow_schema.json setting a minimum o... 010
nf-core @nf-co.re · 28/08/2026Pipeline release! nf-core/airrflow v5.1.1 - 5.1.1 - Ventus Hotfix! Please see the changelog: github.com/nf-core/airrflow/release…github.comRelease 5.1.1 - Ventus Hotfix · nf-core/airrflowFixed #494 Allow passing boolean arguments to Rscript execution from config files. 010
nf-core @nf-co.re · 28/08/2026Curious about the nf-core Hackathon in Barcelona this October?👩💻 Check out hackathon projects and group leaders so far🧵 111
nf-core @nf-co.re · 27/08/2026Pipeline release! nf-core/pairgenomealign v3.0.4 - nf-core/pairgenomealign v3.0.4 – Kuro mitsu! Please see the changelog: github.com/nf-core/pairgenomealign/…github.comRelease nf-core/pairgenomealign v3.0.4 – Kuro mitsu · nf-core/pairgenomealignv3.0.4 "Kuro mitsu" - [August 21st 2026] Fixed Fix a race condition in the collection of alignment statistics (#94). In the full-size test suite, exchange the roles of the two human genomes, and a... 010
nf-core @nf-co.re · 25/08/2026Pipeline release! nf-core/sopa v1.0.1 - 1.0.1! Please see the changelog: github.com/nf-core/sopa/releases/ta…github.comRelease 1.0.1 · nf-core/sopaFixes Set writable env vars for StarDist and Proseg segmentation (#35) Ensure the tests can't silently fail (#29) Updates Support the image_scale parameter (#30) Update the spaceranger module (#... 000
nf-core @nf-co.re · 20/08/2026Pipeline release! nf-core/pixelator v5.0.1 - nf-core/pixelator 5.0.1! Please see the changelog: github.com/nf-core/pixelator/releas…github.comRelease nf-core/pixelator 5.0.1 · nf-core/pixelator[5.0.1] - 2026-08-17 Patches Changed Increase pna_graph_component_size_max_threshold default value to 1M. By @Aratz #243 Documentation Document how to configure DuckDB temporary storage environm... 000
nf-core @nf-co.re · 19/08/2026Pipeline release! nf-core/seqinspector v1.1.2 - nf-core/seqinspector 1.1.2 - Carrie Bishop! Please see the changelog: github.com/nf-core/seqinspector/rel…github.comRelease nf-core/seqinspector 1.1.2 - Carrie Bishop · nf-core/seqinspectorWhat's Changed Back to dev by @FranBonath in #270 Important! Template update for nf-core/tools v4.1.0 by @nf-core-bot in #271 Prepare release v1.1.2 (Template update) by @agrima2010 in #272 Addres... 010
nf-core @nf-co.re · 12/08/2026Pipeline release! nf-core/sarek v3.10.0 - 3.10.0 - Aktse! Please see the changelog: github.com/nf-core/sarek/releases/t…github.comRelease 3.10.0 - Aktse · nf-core/sarek3.10.0 - Aktse Added Addition of: Parabricks HaplotypeCaller with --tools parabricks_haplotypecaller by @gburnett-nvidia. This currently produces per-sample VCFs and does not support joint germlin... 000
nf-core @nf-co.re · 12/08/2026Pipeline release! nf-core/seqinspector v1.1.1 - nf-core/seqinspector 1.1.1 - Cindy Mackenzie! Please see the changelog: github.com/nf-core/seqinspector/rel…github.comRelease nf-core/seqinspector 1.1.1 - Cindy Mackenzie · nf-core/seqinspectorWhat's Changed Back to dev by @maxulysse in #259 Add chelae/trim as an alternate trimming tool by @maxulysse in #260 Remove vulnerable PR-comment artifact pattern by @mashehu in #263 Back-merge th... 000
nf-core @nf-co.re · 11/08/2026Pipeline release! nf-core/magmap v1.2.0 - nf-core/magmap v1.2.0! Please see the changelog: github.com/nf-core/magmap/releases/…github.comRelease nf-core/magmap v1.2.0 · nf-core/magmapWhat's Changed Remove vulnerable PR-comment artifact pattern by @mashehu in #214 Release 1.2.0 by @erikrikarddaniel in #228 Update CHANGELOG for v1.2.0 release date and features by @erikrikarddani... 000
nf-core @nf-co.re · 11/08/2026Pipeline release! nf-core/proteinfamilies v2.5.0 - Zinc Heron! Please see the changelog: github.com/nf-core/proteinfamilies/…github.comRelease Zinc Heron · nf-core/proteinfamiliesAdded #182 - Added an alternative, iterative family generation algorithm, selectable with --family_generation_algorithm iterative. It hands whole chunks of clusters (--clusters_per_chunk) to mgnif... 000
nf-core @nf-co.re · 10/08/2026Pipeline release! nf-core/lsmquant v1.0.3 - 1.0.3 - Excited Squid! Please see the changelog: github.com/nf-core/lsmquant/release…github.comRelease 1.0.3 - Excited Squid · nf-core/lsmquantAdded PR#72 remove local module numorph3dunet and include the updated nf-core/module numorph_3dunet 000
nf-core @nf-co.re · 07/08/2026Pipeline release! nf-core/epitopeprediction v3.1.1 - 3.1.1 - Lustnau Hotfix! Please see the changelog: github.com/nf-core/epitopepredictio…github.comRelease 3.1.1 - Lustnau Hotfix · nf-core/epitopepredictionFixed #369 - Fixed wrong allele annotations in netmhcpan and netmhciipan results by reading allele labels from the prediction output header (#358), and accept any known sub-release of a supported ... 010
nf-core @nf-co.re · 06/08/2026Spaces for the nf-core Hackathon in Barcelona on Oct 15–16 are filling up! 👨💻 Join the local @nextflow.io community to collaborate on projects, from adding new features to building entirely new pipelines. nf-co.re/events/2026/...nf-co.reHackathon - October 2026 (Barcelona)An in-person hackathon held in Barcelona 021
nf-core @nf-co.re · 06/08/2026Pipeline release! nf-core/spatialaxe v1.0.1 - 1.0.1! Please see the changelog: github.com/nf-core/spatialaxe/relea…github.comRelease 1.0.1 · nf-core/spatialaxeHotfix 1.0.1 to tackle the following issues #189 #186 Tackling PRs: #195 #145 What's Changed dev branch version bump to 1.1.0dev by @heylf in #173 Important! Template update for nf-core/tools ... 000
nf-core @nf-co.re · 04/08/2026Pipeline release! nf-core/seqsubmit v1.0.0 - 1.0.0! Please see the changelog: github.com/nf-core/seqsubmit/releas…github.comRelease 1.0.0 · nf-core/seqsubmitInitial release of nf-core/seqsubmit Added The pipeline supports four submission modes via dedicated workflows: mags — Metagenome Assembled Genomes submission (GENOMESUBMIT) bins — Metagenomic bin... 022
nf-core @nf-co.re · 03/08/2026Pipeline release! nf-core/phyloplace v2.1.0 - v2.1.0 - 2026-08-03! Please see the changelog: github.com/nf-core/phyloplace/relea…github.comRelease v2.1.0 - 2026-08-03 · nf-core/phyloplaceAdded #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) 000
nf-core @nf-co.re · 01/08/2026Pipeline release! nf-core/mag v5.5.0 - mag 5.5.0 - Purple Penguin! Please see the changelog: github.com/nf-core/mag/releases/tag…github.comRelease mag 5.5.0 - Purple Penguin · nf-core/magAdded #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... 010
nf-core @nf-co.re · 29/07/2026New blog post! nf-core/tools - 4.1.0 nf-co.re/blog/2026/tools-4_1_0 010
