The nf-core framework for community-curated bioinformatics pipelines.

v3.5.0 - Terne Topi - [2025-11-19]

See more details about this release on our blog: https://nf-co.re/blog/2025/tools-3_5_0

Highlights

• Version reporting with topic channels in modules

General

• Improve file ignores in workflow file enumeration (#3820)
• add optional link to blogpost to sync PR (#3852)
• Avoid deleting files ignored by git during pipelines sync (#3847)
• remove trailing comas from nextflow_schema.json (#3874)
• Make bump-version snapshot test more stable (#3865)
• add missing setup steps to snapshot update action (#3883)
• fix sync test (#3885)
• fix syntax in dockerfile for devcontainer (#3887)
• Enable authenticated pipeline download from nf-core compatible repos with github api (#3607)
• fix pytest setup matrix (#3888)
• Fix GH API rate limits. (#3895)
• devcontainer: downgrade to debian 12 and revert #3904 (#3907)

Template

• Change GitHub Codespaces badge style (#3869 and #3873)
• update multiqc version to fix utils test (#3853)
• Update multiqc to 1.32 (#3878)
• Update pipeline creation information page to be more exclusive as to what should use the full nf-core pipeline template (#3891)
• Fix LSP warnings in pipeline template (#3905)

Linting

• TEMPLATE: ignore nf-core components during prettier linting (#3858)
• update json schema store URL (#3877)
• add word boundary for input, output and topic linting (#3894)
• Add linting of topics (#3902)

Modules

• Add topics to the template + update linting (#3779)
• Preserve the value of self.modules_repo across nested calls (#3881)
• modules lint: handle meta.ymls without topics field (#3909)

Version updates

• Update GitHub Actions (major) (#3849)
• Update docker/setup-qemu-action digest to c7c5346 (#3875)
• chore(deps): update python:3.14-slim docker digest to 9813eec (#3880)
• chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.4 (#3882)
• Update python:3.14-slim Docker digest to 4ed3310 (#3862)
• Update dependency textual-dev to v1.8.0 (#3860)
• Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.3 (#3861)
• Update GitHub Actions (major) (#3849)
• chore(deps): update mcr.microsoft.com/devcontainers/miniconda docker digest to 19516ba (#3890)
• Update dependency textual to v6.6.0 (#3892)
• chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 (#3893)
• Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 (#3900)
• Update actions/checkout digest to 93cb6ef (#3906)