nf-core/newsletter, September 2026

Advisories

• HIGH Merged families use the wrong sample's seed MSAs in proteinfamilies pipeline 2.0.0 - 2.4.0 (Known Regression) — <p>MERGE_FAMILIES:MERGE_SEEDS paired every sample with the first sample’s seed alignments</p>

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/seqsubmit v1.0.0 — nf-core pipeline for data submission to ENA

Pipeline releases

• nf-core/airrflow v5.1.1 (28 Aug 2026)
• nf-core/epitopeprediction v3.1.1 (7 Aug 2026)
• nf-core/fastqrepair v1.1.1 (31 Aug 2026)
• nf-core/lsmquant v1.0.3 (10 Aug 2026)
• nf-core/mag v5.5.0 (1 Aug 2026)
• nf-core/magmap v1.2.0 (11 Aug 2026)
• nf-core/pairgenomealign v3.0.4 (26 Aug 2026)
• nf-core/phyloplace v2.1.0 (3 Aug 2026)
• nf-core/pixelator v5.0.1 (20 Aug 2026)
• nf-core/proteinfamilies v2.5.0 (11 Aug 2026)
• nf-core/sarek v3.10.0 (12 Aug 2026)
• nf-core/seqinspector v1.1.1, v1.1.2 (19 Aug 2026)
• nf-core/sopa v1.0.1 (25 Aug 2026)
• nf-core/spatialaxe v1.0.1 (6 Aug 2026)

Upcoming events

• Bytesize Bytesize: nf-core/nft-utils — 2 Sept 2026
  <p>Louis Le Nezet</p>
• Hackathon Hackathon - October 2026 (Barcelona) — 15 Oct 2026 – 16 Oct 2026
  <p>An in-person hackathon held in Barcelona</p>

In case you missed it

Recent events

• Bytesize: nf-meta — 11 Aug 2026 (Bytesize)
• Hackathon - Agosto 2026 — 15 Aug 2026 – 16 Aug 2026 (Hackathon)
• Bytesize: nf-core/longraredisease — 18 Aug 2026 (Bytesize)
• Bytesize: nf-core/drop — 25 Aug 2026 (Bytesize)

Earlier blog posts

• nf-core/tools - 4.1.0 — 29 Jul 2026
• Maintainers Minutes: May - June 2026 — 1 Jul 2026
• Introducing the nf-core newsletter — 23 Jun 2026

Earlier advisories

• CRITICAL Remote code execution and bot token theft via the pipeline template's PR-comment workflow — 23 Jul 2026

New pipelines & proposals

Pipeline proposals

From nf-core/proposals.

• nf-core/grnintegrate — Accepted (#159)
• nf-core/snv-sort-and-fold — Accepted (#148)
• nf-core/gap-flow — New (#166)
• nf-core/taxmarker — New (#165)
• nf-core/stamp — New (#164)
• nf-core/<geomx-dsp> — New (#163)
• nf-core/plasmodiumpopgen — New (#161)
• nf-core/fragmentomics — New (#160)