# nf-core/newsletter, July 2025

2 blog posts, 12 pipeline releases, 2 upcoming events.

[View on the nf-core website](https://nf-co.re/newsletter/2025/07)

## Blog posts

- [nf-core/tools - 3.3](https://nf-co.re/blog/2025/tools-3_3) — An nf-testic release
  _3 Jun 2025 · by mashehu, mirpedrol_
- [Maintainers Minutes: May 2025](https://nf-co.re/blog/2025/maintainers-minutes-2025-05-30) — Keeping you informed of the latest maintainers discussions
  _3 Jun 2025 · by maxulysse_

## New pipeline first releases 🎉

These pipelines just had their very first release.

- [nf-core/createtaxdb](https://nf-co.re/createtaxdb) v1.0.0 — Parallelised and automated construction of metagenomic classifier databases of different tools
- [nf-core/pathogensurveillance](https://nf-co.re/pathogensurveillance) v1.0.0 — Surveillance of pathogens using population genomics and sequencing

## Pipeline releases

- [nf-core/airrflow](https://nf-co.re/airrflow) v4.3.1 _(9 Jun 2025)_
- [nf-core/bamtofastq](https://nf-co.re/bamtofastq) v2.2.0 _(17 Jun 2025)_
- [nf-core/demo](https://nf-co.re/demo) v1.0.2 _(27 Jun 2025)_
- [nf-core/metatdenovo](https://nf-co.re/metatdenovo) v1.2.0 _(18 Jun 2025)_
- [nf-core/oncoanalyser](https://nf-co.re/oncoanalyser) v2.1.0 _(30 Jun 2025)_
- [nf-core/pixelator](https://nf-co.re/pixelator) v2.0.0 _(24 Jun 2025)_
- [nf-core/proteinfamilies](https://nf-co.re/proteinfamilies) v1.2.0 _(16 Jun 2025)_
- [nf-core/raredisease](https://nf-co.re/raredisease) v2.6.0 _(25 Jun 2025)_
- [nf-core/rnaseq](https://nf-co.re/rnaseq) v3.19.0 _(10 Jun 2025)_
- [nf-core/scnanoseq](https://nf-co.re/scnanoseq) v1.2.0 _(9 Jun 2025)_

## Upcoming events

- **Talk** [Bytesize: nf-core test-datasets](https://nf-co.re/events/2025/bytesize_nfcore_testdatasets) — 8 Jul 2025
  Julian Flesch, QBiC, University Tübingen
- **Talk** [#animal-genomics: July Meeting](https://nf-co.re/events/2025/sig_animalgenomics_jul) — 16 Jul 2025
  Luca Fontanesi (Full Professor of animal breeding and genetics at the University of Bologna)

## In case you missed it

### Recent events

- [Bytesize: nf-core/rangeland](https://nf-co.re/events/2025/bytesize_rangeland) — 10 Jun 2025 (Talk)
- [meta-omics nf-test fest](https://nf-co.re/events/2025/sig_metaomics_nftestfest) — 11 Jun 2025 – 12 Jun 2025 (Training)
- [Introduction to nf-core/airrflow](https://nf-co.re/events/2025/training_nf-core-airrflow_june) — 12 Jun 2025 (Training)
- [#animal-genomics: June Meeting](https://nf-co.re/events/2025/sig_animalgenomics_jun) — 18 Jun 2025 (Talk)
- [Nextflow Training Week - June 2025](https://nf-co.re/events/2025/training-week-q2) — 23 Jun 2025 – 27 Jun 2025 (Training)

### Earlier blog posts

- [nf-core supports now `main` branch names](https://nf-co.re/blog/2025/switching-master-to-main) — 19 May 2025
- [Maintainers Minutes: April 2025](https://nf-co.re/blog/2025/maintainers-minutes-2025-04-24) — 2 May 2025
- [State of the nf-core CI](https://nf-co.re/blog/2025/state-of-nf-core-ci) — 9 Apr 2025

### Earlier advisories

- **HIGH** [.command.run Permission denied](https://nf-co.re/advisories/process-shell-configuration) — 15 May 2025

## New pipelines & proposals

### New pipeline repositories

- [nf-core/panoramaseq](https://nf-co.re/panoramaseq) _(in development)_ — a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays

### Pipeline proposals

From [nf-core/proposals](https://github.com/nf-core/proposals/issues).

- [nf-core/locusassembly](https://github.com/nf-core/proposals/issues/52) — Accepted (#52)
- [nf-core/tcrpmhcbinding](https://github.com/nf-core/proposals/issues/50) — Accepted (#50)
- [nf-core/viralmetagenome - untargeted viral genome reconstruction](https://github.com/nf-core/proposals/issues/28) — Accepted (#28)
- [nf-core/metabiomx](https://github.com/nf-core/proposals/issues/58) — New (#58)
- [nf-core/consepopgen](https://github.com/nf-core/proposals/issues/57) — New (#57)
- [nf-core/SNP_clustering](https://github.com/nf-core/proposals/issues/56) — New (#56)
- [nf-core/netzoo](https://github.com/nf-core/proposals/issues/55) — New (#55)

### Other proposals

- [New RFC:  Introducing "Advisories" as a new content type for structured issue reporting](https://github.com/nf-core/proposals/issues/44) — Accepted (#44)
- [New RFC: Migrate Subworkflows and Template boilerplate to nf-core-utils plugin](https://github.com/nf-core/proposals/issues/51) — New (#51)
- [New RFC: Use Trunk-based Development](https://github.com/nf-core/proposals/issues/49) — New (#49)
- [New RFC:  using references](https://github.com/nf-core/proposals/issues/48) — New (#48)
- [New RFC:  Switching from `publishDir` to workflow output](https://github.com/nf-core/proposals/issues/47) — New (#47)
- [New RFC: switching to topic channels for collecting versions](https://github.com/nf-core/proposals/issues/46) — New (#46)

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