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

v3.5.2 - Terne Topi Patch 2 - [2026-01-30]

General

• Switch from pre-commit to prek for pre-commit hooks in development(#3899)
• Fix docker errors in test (#3924)
• switch to uv and pyproject.toml (#3925)
• dockerhub action: add disk clean-up step and combine the two actions (#3926)
• Pin j178/prek-action action to 91fd7d7 (#3931)
• Simplify coverage reporting in pytest.yml (#3934)
• add pre-commit hook to keep uv.lock in sync (#3933)
• Fix quote handling in meta.yml (#3948)
• Add support for SVG files in bump-version command (#3978)
• handle type for val in topics correctly (#3991)
• Update docker/login-action digest to c94ce9f (#3998)
• fix wrong parsing when output values contain spaces (#3999)
• fix failing devcontainer builds (#4013)

Linting

• fix test for linting for version.yml (#3947)
• Fix bugs in subworkflows lint causing false positive warnings (#3968)
• more fixes for incorrect parsing of version statement (#3973)
• handle val in version topics correctly (#3988)
• handle additional attributes in input parsing correctly (#3990)

Modules

• sort meta.yml based on keys in schema (#3958)
• fix(modules_json): Use name string instead of dict as key in recreate_dependencies (#3963)
• linting: polish regex for output parsing in modules main.nf (#3967)
• modules linting: catch failing edamontology requests (#3994)

Subworkflows

• Update to new topic version handling (#3929)

Version updates

• Update actions/setup-python digest to 83679a8 (#3928)
• Update python:3.14-slim Docker digest to 119fd5b (#3910)
• Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 (#3943)
• Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a (#3946)
• Update actions/checkout digest to 8e8c483 (#3956)
• Update GitHub Actions (#3957)
• Update astral-sh/setup-uv digest to ed21f2f (#3959)
• Update codecov/codecov-action digest to 671740a (#3962)
• Update codecov/codecov-action digest to 671740a (#4000)
• Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 (#4007)
• Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 (#4006)
• Update dependency textual-dev to v1.8.0 (#4005)
• Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 (#4002)
• Update dependency textual to v7 (#4008)
• Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a29f1c (#4009)
• Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 (#4011)
• Update python:3.14-slim Docker digest to 9b81fe9 (#4012)