nf-core/newsletter, November 2026

Blog posts

• nf-core/tools - 4.2.{0,1} — Next stop: pipeline metro maps
  21 Oct 2026 · by mashehu

  

• Kicking off the Benchmarking SIG Monthly Meetings — Join us for our new monthly meetings, starting with variant benchmarking
  15 Oct 2026 · by kubranarci, georgiakes

  

Advisories

• HIGH Secrets in the debug log artifact of the AWS test workflows (Security) — The AWS test workflows in the pipeline template uploaded a debug log containing secrets as a public workflow artifact, letting anyone signed in to GitHub read them
• CRITICAL Bot token theft via the pipeline template's fix-linting workflow (Security) — A workflow in the pipeline template ran a contributor's own lint configuration with access to a shared bot token, letting an outside attacker run code on nf-core's CI and steal the token

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/bacmodel v1.0.0, v1.0.1 — Systems-based bacterial functional modeling pipeline
• nf-core/datasync v1.0.0, v1.0.1, v1.0.2 — nf-core/datasync is a system operation pipeline that provides several workflows for handling system operation / automation tasks
• nf-core/plasmodiumdrugres v1.0.0 — Pipeline for analyzing drug resistance markers from Plasmodium microhaplotype data. Translates variants into amino acid changes at drug resistance loci and estimates allele frequencies and prevalences at both single-locus and multi-locus levels. Microhaplotype data can be supplied in the form of an allele table or a PMO file.
• nf-core/provenancereport v1.0.0 — Generate reproducible Quarto reports together with an audit trail of inputs, checksums, software versions, runtime environments, and provenance metadata.
• nf-core/tumourevo v1.0.0 — Analysis pipeline to model tumour clonal evolution from WGS data (driver annotation, quality control of copy number calls, subclonal and mutational signature deconvolution)

Pipeline releases

• nf-core/airrflow v5.1.2 (10 Oct 2026)
• nf-core/ampliseq v3.0.0, v3.1.0 (28 Oct 2026)
• nf-core/detaxizer v1.4.0 (26 Oct 2026)
• nf-core/drugresponseeval v1.3.0 (12 Oct 2026)
• nf-core/epitopeprediction v3.2.0 (15 Oct 2026)
• nf-core/genomeassembler v2.0.1 (23 Oct 2026)
• nf-core/magmap v1.3.0, v1.3.1 (22 Oct 2026)
• nf-core/metatdenovo v2.0.0 (7 Oct 2026)
• nf-core/mhcquant v3.3.0 (2 Oct 2026)
• nf-core/pixelator v5.0.3 (7 Oct 2026)
• nf-core/proteinfamilies v2.6.0 (1 Oct 2026)
• nf-core/rnasplice v2.0.0 (20 Oct 2026)
• nf-core/rnastructurome v1.1.0 (23 Oct 2026)
• nf-core/sarek v3.11.0 (26 Oct 2026)
• nf-core/stableexpression v1.1.0 (7 Oct 2026)
• nf-core/variantbenchmarking v1.6.0 (30 Oct 2026)

In case you missed it

Recent events

• Hackathon - October 2026 (Barcelona) — 15 Oct 2026 – 16 Oct 2026 (Hackathon)
• Bytesize: nf-core/hackathon October 2026 Wrap-up — 21 Oct 2026 (Bytesize)
• #animal-genomics: October Meeting — 21 Oct 2026 (Talk)

Earlier advisories

• HIGH Merged families use the wrong sample's seed MSAs in proteinfamilies pipeline 2.0.0 - 2.4.0 — 11 Aug 2026

New pipelines & proposals

Pipeline proposals

From nf-core/proposals.

• nf-core/genomeannotation — Accepted (#169)
• nf-core/stampseq — Accepted (#164)
• nf-core/eupathpopgen — Accepted (#161)
• nf-core/glpopgen — Accepted (#156)
• nf-core/rami2d — New (#187)
• nf-core/pitisfinder — New (#186)
• nf-core/ont_dap — New (#185)
• nf-core/sifts — New (#184)
• nf-core/sherlock — New (#183)
• nf-core/deconflow — New (#182)
• nf-core/beav — New (#181)
• nf-core/sangerseq — New (#180)
• nf-core/kanata — New (#179)
• nf-core/pira — New (#177)
• nf-core/oncoseq — New (#176)
• nf-core/rnadegradome — New (#175)
• nf-core/dapseq — New (#174)