nf-core/newsletter, July 2025

Blog posts

• nf-core/tools - 3.3 — An nf-testic release
  3 Jun 2025 · by mashehu, mirpedrol

  

• Maintainers Minutes: May 2025 — 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 v1.0.0 — Parallelised and automated construction of metagenomic classifier databases of different tools
• nf-core/pathogensurveillance v1.0.0 — Surveillance of pathogens using population genomics and sequencing

Pipeline releases

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

Upcoming events

• Talk Bytesize: nf-core test-datasets — 8 Jul 2025
  Julian Flesch, QBiC, University Tübingen
• Talk #animal-genomics: July Meeting — 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 — 10 Jun 2025 (Talk )
• meta-omics nf-test fest — 11 Jun 2025 – 12 Jun 2025 (Training )
• Introduction to nf-core/airrflow — 12 Jun 2025 (Training )
• #animal-genomics: June Meeting — 18 Jun 2025 (Talk )
• Nextflow Training Week - June 2025 — 23 Jun 2025 – 27 Jun 2025 (Training )

Earlier blog posts

• nf-core supports now `main` branch names — 19 May 2025
• Maintainers Minutes: April 2025 — 2 May 2025
• State of the nf-core CI — 9 Apr 2025

Earlier advisories

• HIGH .command.run Permission denied — 15 May 2025

New pipelines & proposals

New pipeline repositories

• nf-core/panoramaseq (in development) — a pipeline to process sequencing based spatial transccriptomics data from in-situ arrays

Pipeline proposals

From nf-core/proposals.

• nf-core/locusassembly — Accepted (# 52)
• nf-core/tcrpmhcbinding — Accepted (# 50)
• nf-core/viralmetagenome - untargeted viral genome reconstruction — Accepted (# 28)
• nf-core/metabiomx — New (# 58)
• nf-core/consepopgen — New (# 57)
• nf-core/SNP_clustering — New (# 56)
• nf-core/netzoo — New (# 55)

Other proposals

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