nf-core/newsletter, October 2025

Blog posts

• Running nf-core pipelines on Google Colab — A guide to running and interacting with nf-core pipelines using Colab and VS Code
  2 Sept 2025 · by KurayiChawatama

  

Advisories

• HIGH Final family representative sequences are faulty in proteinfamilies pipeline 1.3.0 (Known Regression) — Bug inside the extract_family_reps.py script of v1.3.0

Pipeline releases

• nf-core/mag v5.0.0 (30 Sept 2025)
• nf-core/oncoanalyser v2.2.0 (2 Sept 2025)
• nf-core/pixelator v2.1.0 (17 Sept 2025)
• nf-core/proteinfamilies v1.3.1 (23 Sept 2025)
• nf-core/rnafusion v4.0.0 (19 Sept 2025)
• nf-core/rnaseq v3.21.0 (18 Sept 2025)
• nf-core/rnavar v1.2.1 (23 Sept 2025)
• nf-core/scnanoseq v1.2.1 (2 Sept 2025)

Upcoming events

• Talk #animal-genomics: October Meeting — 15 Oct 2025
  Daniela Lourenco (University of Georgia, USA)
• Hackathon Hackathon - October 2025 (Barcelona) — 28 Oct 2025 – 29 Oct 2025
  An in-person hackathon held in Barcelona
• Talk Bytesize: nf-core/mag v5.0 — 28 Oct 2025
  Diego Alvarez Saravia, University of Magallanes
• Talk Bytesize: The Nextflow plugin registry — 11 Nov 2025
  Phil Ewels, Seqera
• Talk #animal-genomics: Meeting — 19 Nov 2025
  Ekaterina Osipova (Harvard University)
• Talk Bytesize: nf-core pipeline template walk through V2 — 25 Nov 2025
  Júlia Mir Pedrol, CRG

In case you missed it

Recent events

• Bytesize: nf-core/createtaxdb — 9 Sept 2025 (Talk )
• Bytesize: RFCs — 16 Sept 2025 (Talk )
• #animal-genomics: September Meeting — 17 Sept 2025 (Talk )

Earlier blog posts

• Maintainers Minutes: August 2025 — 31 Aug 2025
• Why are my pipeline download tests failing? — 28 Aug 2025
• Introducing nf-core Advisories — 21 Aug 2025
• Empowering bioinformatics communities with Nextflow and nf-core — 6 Aug 2025
• Maintainers Minutes: July 2025 — 31 Jul 2025
• Meet the new meta.yml — 7 Jul 2025

New pipelines & proposals

New pipeline repositories

• nf-core/pacsomatic (in development) — Nextflow pipeline for PacBio HiFi tumor/normal somatic genomics

Pipeline proposals

From nf-core/proposals.

• nf-core/seqsubmit — Accepted (# 79)
• nf-core/nf-segmented — Accepted (# 74)
• nf-core/thetis — Accepted (# 66)
• nf-core/longraredisease — Accepted (# 64)
• nf-core/consepopgen — Accepted (# 57)
• nf-core/hpc-dock-bench — New (# 84)
• nf-core/cageflow — New (# 83)
• nf-core/provacseq — New (# 82)
• nf-core/proteindesign — New (# 81)
• nf-core/genomicvista — New (# 80)
• nf-core/mspepid — New (# 78)

Other proposals

• Test RFC: Python Approval System — Accepted (# 87)
• New RFC: add nf-co2footprint plugin to the template — Accepted (# 72)
• nf-core/pacsomatic: comprehensive somatic analysis using Pacbio HiFi read data — Accepted (# 63)
• New RFC: Pipeline maturity model (Very Important Pipelines) — New (# 89)
• New RFC: use process directives to declare prefix, args and when defaults — New (# 86)
• New RFC: PR master Improvements — New (# 85)