nf-core/newsletter, August 2026

Blog posts

• nf-core/tools - 4.1.0 — Fast containers without any oxidation
  29 Jul 2026 · by mashehu

  

• Maintainers Minutes: May - June 2026 — Keeping you informed of the latest maintainers discussions
  1 Jul 2026 · by maxulysse

  

Advisories

• CRITICAL Remote code execution and bot token theft via the pipeline template's PR-comment workflow (Security) — A workflow in the pipeline template ran a value taken from a contributor's pull request as a command, letting an outside attacker run code on nf-core's CI and steal a shared bot token

New pipeline first releases 🎉

These pipelines just had their very first release.

• nf-core/mcmicro v2.0.0 — An end-to-end processing pipeline that transforms multi-channel whole-slide images into single-cell data.
• nf-core/sopa v1.0.0 — Nextflow version of Sopa - spatial omics pipeline and analysis

Pipeline releases

• nf-core/createtaxdb v3.1.0 (3 Jul 2026)
• nf-core/pairgenomealign v3.0.2, v3.0.3 (28 Jul 2026)
• nf-core/pixelator v5.0.0 (16 Jul 2026)
• nf-core/raredisease v3.1.2 (6 Jul 2026)
• nf-core/scrnaseq v4.2.0 (4 Jul 2026)
• nf-core/seqinspector v1.1.0 (14 Jul 2026)
• nf-core/viralmetagenome v1.1.3 (2 Jul 2026)

Upcoming events

• Talk Bytesize: nf-meta — 11 Aug 2026
  Julian Flesch, QBiC
• Hackathon Hackathon - Agosto 2026 — 15 Aug 2026 – 16 Aug 2026
  Um hackathon presencial para contribuir com tarefas do nf-core e de seus projetos Nextflow
• Talk Bytesize: nf-core/longraredisease — 18 Aug 2026
  Nour Mahfel, University of Birmingham
• Talk Bytesize: nf-core/drop — 25 Aug 2026
  Ata Jadid Ahari, Nicolas Vannieuwkerke

In case you missed it

Earlier blog posts

• Introducing the nf-core newsletter — 23 Jun 2026
• Why parameters are strings all of a sudden — 26 May 2026

New pipelines & proposals

New pipeline repositories

• nf-core/daamicrobiome (in development) — Microbiome differential abundance consensus pipeline
• nf-core/pathogenepidemiology (in development) — [UNDER DEVELOPMENT] A profile-based pipeline for genomic epidemiological analysis of predefined pathogens.

Pipeline proposals

From nf-core/proposals.

• nf-core/primeridentifier — Accepted (#152)
• nf-core/cfmultiomics — Accepted (#144)
• dragen — Accepted (#137)
• nf-core/pathogenepidemiology — Accepted (#134)
• nf-core/transporter — Accepted (#126)
• nf-core/epigenomeanalyser — New (#158)
• nf-core/<vasta> — New (#157)
• nf-core/glpopgen — New (#156)
• nf-core/strcalling — New (#155)
• nf-core/atacportray — New (#153)

Other proposals

• New RFC: use process directives to declare prefix, args and when defaults — Accepted (#86)