nf-core/newsletter, December 2025

Blog posts

• The Mass Spectrometry Proteomics Special Interest Group — Unifying efforts for mass spectrometry data analysis in nf-core
  26 Nov 2025 · by DongzeHe

  

• nf-core/tools - 3.5.0 — Hot topic release
  19 Nov 2025 · by mashehu, mirpedrol

  

• Topic: Topics — How to adopt Topic channels in your favorite nf-core module
  19 Nov 2025 · by mapo9, nvnieuwk, mribeirodantas, kobelavaerts, wangdepin, yadavbha, eit-maxlcummins

  

• The nf-core roadmap for adopting the new Nextflow syntax — Not DSL3
  17 Nov 2025 · by mirpedrol, mashehu

  

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/magmap v1.0.0 — Best-practice analysis pipeline for mapping reads to a (large) collections of genomes

Pipeline releases

• nf-core/createtaxdb v2.0.0 (14 Nov 2025)
• nf-core/detaxizer v1.3.0 (14 Nov 2025)
• nf-core/epitopeprediction v3.1.0 (21 Nov 2025)
• nf-core/mag v5.2.0 (7 Nov 2025)
• nf-core/methylong v2.0.0 (21 Nov 2025)
• nf-core/pixelator v2.2.0 (5 Nov 2025)
• nf-core/proteinfamilies v2.1.0 (25 Nov 2025)
• nf-core/rnafusion v3.0.1b (14 Nov 2025)
• nf-core/rnaseq v3.22.0 (27 Nov 2025)
• nf-core/taxprofiler v1.2.5 (21 Nov 2025)
• nf-core/viralmetagenome v1.0.0 (4 Nov 2025)

Upcoming events

• Talk Bytesize: topic channels in nf-core/modules — 2 Dec 2025
  Nicolas Vannieuwkerke, Center for Medical Genetics Ghent
• Training Introduction to nf-core/airrflow — 4 Dec 2025
  Introductory practical workshop to nf-core/airrflow
• Talk Bytesize: nf-core/reportho — 9 Dec 2025
  Igor Trujnara, Institute for Research in Biomedicine / Barcelona Supercomputing Center, Barcelona
• Talk Bytesize: Migrating to workflow outputs — 27 Jan 2026
  Chris Hakkaart, Seqera

In case you missed it

Recent events

• Bytesize: The Nextflow plugin registry — 11 Nov 2025 (Talk )
• #animal-genomics: Meeting — 19 Nov 2025 (Talk )
• Bytesize: nf-core pipeline template walk through V2 — 25 Nov 2025 (Talk )

Earlier blog posts

• nf-core core team retreat - September 2025 — 20 Oct 2025
• nf-core/tools - 3.4.0 — 16 Oct 2025
• Running nf-core pipelines on Google Colab — 2 Sept 2025

Earlier advisories

• HIGH Final family representative sequences are faulty in proteinfamilies pipeline 1.3.0 — 29 Sept 2025

New pipelines & proposals

Pipeline proposals

From nf-core/proposals.

• nf-core/xmir — Accepted (# 101)
• nf-core/mdsimulations — Accepted (# 99)
• nf-core/genephylo — Accepted (# 98)
• nf-core/tandemrepeat — Accepted (# 94)
• nf-core/cageflow — Accepted (# 83)
• nf-core/netzoo — Accepted (# 55)
• nf-core/protaga — New (# 102)
• nf-core/musa — New (# 97)

Other proposals

• New special interest group: Proteomics Interest Group — Accepted (# 100)
• New RFC: EESSI/EasyBuild and nf-core — New (# 103)