nf-core/newsletter, June 2025

Blog posts

• nf-core supports now `main` branch names — Announcing the possibility to change a pipeline default branch to main
  19 May 2025 · by mirpedrol, jfy133

  

• Maintainers Minutes: April 2025 — Keeping you informed of the latest maintainers discussions
  2 May 2025 · by jfy133

  

Advisories

• HIGH .command.run Permission denied (Incompatibility) — Nextflow versions after 24.10.6 are incompatible with certain nf-core pipelines published in 2024 and early 2025.

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/methylong v1.0.0 — Extract methylation calls from long reads (ONT/ PacBio)

Pipeline releases

• nf-core/ampliseq v2.14.0 (23 May 2025)
• nf-core/coproid v2.0.0 (22 May 2025)
• nf-core/epitopeprediction v3.0.0 (9 May 2025)
• nf-core/mag v4.0.0 (22 May 2025)
• nf-core/mhcquant v3.0.0 (22 May 2025)
• nf-core/multiplesequencealign v1.1.1 (27 May 2025)
• nf-core/nascent v2.3.0 (8 May 2025)
• nf-core/pairgenomealign v2.1.0 (16 May 2025)
• nf-core/proteinfamilies v1.1.0, v1.1.1 (20 May 2025)
• nf-core/raredisease v2.5.0 (22 May 2025)

Upcoming events

• Talk Bytesize: nf-core/rangeland — 10 Jun 2025
  Felix Kummer, Humboldt-Universität zu Berlin
• Training meta-omics nf-test fest — 11 Jun 2025 – 12 Jun 2025
  Hackathon to implement nf-test in meta-omics related pipelines!
• Training Introduction to nf-core/airrflow — 12 Jun 2025
  Introductory practical workshop to nf-core/airrflow
• Talk #animal-genomics: June Meeting — 18 Jun 2025
  Ángela Cánovas (Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada)
• Training Nextflow Training Week - June 2025 — 23 Jun 2025 – 27 Jun 2025
  Join the Nextflow Training Week in June
• 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/fastqrepair — 13 May 2025 (Talk )
• Hackathon - May 2025 (Boston) — 13 May 2025 – 14 May 2025 (Hackathon )
• #animal-genomics: May Meeting — 21 May 2025 (Talk )

Earlier blog posts

• State of the nf-core CI — 9 Apr 2025
• nf-core survey 2025: the results — 26 Mar 2025
• Spring cleaning 2025 — 20 Mar 2025
• nf-core weekly help desk is coming to Asia-Pacific! — 10 Mar 2025

New pipelines & proposals

New pipeline repositories

• nf-core/alleleexpression (in development) — Alleleexpression is a nf-core pipeline for allele-specific expression (ASE) analysis using STAR-WASP for alignment, UMI-tools for deduplication, and phaser for haplotype phasing and ASE detection.
• nf-core/cellpainting (in development) —
• nf-core/longraredisease — Long read sequencing pipeline to identify variants in patients with neurodevelopmental disorders

Pipeline proposals

From nf-core/proposals.

• nf-core/panoramaseq — Accepted (# 20)
• nf-core/longrnaseq — New (# 29)
• nf-core/viralmetagenome - untargeted viral genome reconstruction — New (# 28)
• nf-core/dbcan — New (# 27)
• nf-core/taxonomicfiltering — New (# 26)
• nf-core/rsvrecon — New (# 25)
• nf-core/methflow — New (# 24)
• nf-core/mitnanex — New (# 22)

Other proposals

• New RFC: New nf-core RFC system for major initiatives — Accepted (# 30)
• New RFC: Introducing "Advisories" as a new content type for structured issue reporting — New (# 44)
• New RFC: CODEOWNER for pipelines — New (# 40)
• New RFC: `main.nf` for each nextflow script — New (# 39)