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Merged
mashehu merged 9 commits into from
Nov 19, 2025
Merged

bump to 3.5.0 #3884

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7052a41
bump to 3.5.0
mashehu Nov 7, 2025
cbde4bb
Merge branch 'dev' into bump-to-3.5.0
mashehu Nov 7, 2025
312b7c6
Merge branch 'dev' into bump-to-3.5.0
mashehu Nov 10, 2025
3c22494
Update CHANGELOG.md
mashehu Nov 11, 2025
af0df28
Merge branch 'dev' into bump-to-3.5.0
mashehu Nov 11, 2025
2290f0d
Merge branch 'dev' into bump-to-3.5.0
mashehu Nov 12, 2025
8404760
Merge branch 'dev' into bump-to-3.5.0
mashehu Nov 18, 2025
ab8bcab
update changelog
mashehu Nov 19, 2025
2c299eb
update changelog title
mashehu Nov 19, 2025
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2 changes: 1 addition & 1 deletion .devcontainer/devcontainer.json
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@@ -1,6 +1,6 @@
{
"name": "nfcore",
"image": "nfcore/devcontainer:dev",
"image": "nfcore/devcontainer:latest",

"remoteEnv": {
// Workspace path on the host for mounting with docker-outside-of-docker
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36 changes: 18 additions & 18 deletions CHANGELOG.md
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@@ -1,40 +1,26 @@
# nf-core/tools: Changelog

## v3.5.0dev
## [v3.5.0 - Terne Topi](https://github.com/nf-core/tools/releases/tag/3.5.0) - [2025-11-19]

### General

- Improve file ignores in workflow file enumeration ([#3820](https://github.com/nf-core/tools/pull/3820))
- Update GitHub Actions (major) ([#3849](https://github.com/nf-core/tools/pull/3849))
- add optional link to blogpost to sync PR ([#3852](https://github.com/nf-core/tools/pull/3852))
- update multiqc version to fix utils test ([#3853](https://github.com/nf-core/tools/pull/3853))
- Update dependency textual to v6.5.0 ([#3859](https://github.com/nf-core/tools/pull/3859))
- Update python:3.14-slim Docker digest to 4ed3310 ([#3862](https://github.com/nf-core/tools/pull/3862))
- Update dependency textual-dev to v1.8.0 ([#3860](https://github.com/nf-core/tools/pull/3860))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.3 ([#3861](https://github.com/nf-core/tools/pull/3861))
- Avoid deleting files ignored by git during `pipelines sync` ([#3847](https://github.com/nf-core/tools/pull/3847))
- remove trailing comas from nextflow_schema.json ([#3874](https://github.com/nf-core/tools/pull/3874))
- Make bump-version snapshot test more stable ([#3865](https://github.com/nf-core/tools/pull/3865))
- Update docker/setup-qemu-action digest to c7c5346 ([#3875](https://github.com/nf-core/tools/pull/3875))
- chore(deps): update python:3.14-slim docker digest to 9813eec ([#3880](https://github.com/nf-core/tools/pull/3880))
- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.14.4 ([#3882](https://github.com/nf-core/tools/pull/3882))
- add missing setup steps to snapshot update action ([#3883](https://github.com/nf-core/tools/pull/3883))
- fix sync test ([#3885](https://github.com/nf-core/tools/pull/3885))
- fix syntax in dockerfile for devcontainer ([#3887](https://github.com/nf-core/tools/pull/3887))
- Enable authenticated pipeline download from nf-core compatible repos with github api ([#3607](https://github.com/nf-core/tools/pull/3607))
- fix pytest setup matrix ([#3888](https://github.com/nf-core/tools/pull/3888))
- chore(deps): update mcr.microsoft.com/devcontainers/miniconda docker digest to 19516ba ([#3890](https://github.com/nf-core/tools/pull/3890))
- Update dependency textual to v6.6.0 ([#3892](https://github.com/nf-core/tools/pull/3892))
- chore(deps): update mcr.microsoft.com/devcontainers/base:debian docker digest to 2e826a6 ([#3893](https://github.com/nf-core/tools/pull/3893))
- Fix GH API rate limits. ([#3895](https://github.com/nf-core/tools/pull/3895))
- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.5 ([#3900](https://github.com/nf-core/tools/pull/3900))
- devcontainer: Set `moby: false` to fix trixie builds ([#3904](https://github.com/nf-core/tools/pull/3904))
- Update actions/checkout digest to 93cb6ef ([#3906](https://github.com/nf-core/tools/pull/3906))
- devcontainer: downgrade to debian 12 and revert `moby:false` ([#3907](https://github.com/nf-core/tools/pull/3907))
- devcontainer: downgrade to debian 12 and revert [#3904](https://github.com/nf-core/tools/pull/3904) ([#3907](https://github.com/nf-core/tools/pull/3907))

### Template

- Change GitHub Codespaces badge style ([#3869](https://github.com/nf-core/tools/pull/3869) and [#3873](https://github.com/nf-core/tools/pull/3873))
- update multiqc version to fix utils test ([#3853](https://github.com/nf-core/tools/pull/3853))
- Update multiqc to 1.32 ([#3878](https://github.com/nf-core/tools/pull/3878))
- Update pipeline creation information page to be more exclusive as to what should use the full nf-core pipeline template ([#3891](https://github.com/nf-core/tools/pull/3891))
- Fix LSP warnings in pipeline template ([#3905](https://github.com/nf-core/tools/pull/3905))
Expand All @@ -52,7 +38,21 @@
- Preserve the value of self.modules_repo across nested calls ([#3881](https://github.com/nf-core/tools/pull/3881))
- modules lint: handle meta.ymls without topics field ([#3909](https://github.com/nf-core/tools/pull/3909))

### Subworkflows
### Version updates

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

## [v3.4.1 - Ducol Dingo Patch 1](https://github.com/nf-core/tools/releases/tag/3.4.1) - [2025-10-16]

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2 changes: 1 addition & 1 deletion setup.py
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from setuptools import find_packages, setup

version = "3.5.0dev"
version = "3.5.0"

with open("README.md") as f:
readme = f.read()
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