bump to 3.6.0dev

.github/RELEASE_CHECKLIST.md

@@ -4,7 +4,7 @@
 2. Most importantly, pick an undeniably outstanding [name](http://www.codenamegenerator.com/) for the release where _Prefix_ = _Metal_ and _Dictionary_ = _Animal_.
 3. Check the [pipeline health page](https://nf-co.re/pipeline_health) to make sure that all repos look sane (missing `TEMPLATE` branches etc)
 4. Check that modules/subworkflows in template are up to date with the latest releases
-5. Create a PR to `dev` to bump the version in `CHANGELOG.md` and `pyproject.toml`.
+5. Create a PR to `dev` to bump the version in `CHANGELOG.md`. `pyproject.toml` and in `uv.lock` (by running `uv sync`).
 6. Make sure all CI tests are passing!
 7. Create a PR from `dev` to `main`
 8. Run a manual sync on `nf-core/testpipeline` and check that CI is passing on the resulting PR: use the `Sync template` GitHub Action from the tools repository specifying the pipeline name and running from the `dev` branch.
@@ -22,4 +22,4 @@
 3. Manually trigger the `Sync template` GitHub Action for all pipelines.
 4. Check that the automatic `PyPi` deployment has worked: [pypi.org/project/nf-core](https://pypi.org/project/nf-core/)
 5. Check `BioConda` has an automated PR to bump the version, and merge. eg. [bioconda/bioconda-recipes #20065](https://github.com/bioconda/bioconda-recipes/pull/20065)
-6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md` and `pyproject.toml`.
+6. Create a tools PR to `dev` to bump back to the next development version in `CHANGELOG.md`, `pyproject.toml` and in `uv.lock` (by running `uv sync`).

CHANGELOG.md

@@ -1,5 +1,19 @@
 # nf-core/tools: Changelog
 
+## v3.6.0dev
+
+### General
+
+### Linting
+
+### Modules
+
+### Subworkflows
+
+### Pipeline template
+
+#### Version updates
+
 ## v3.5.2
 
 ### General
@@ -8,37 +22,15 @@
 - Fix docker errors in test ([#3924](https://github.com/nf-core/tools/pull/3924))
 - switch to uv and pyproject.toml ([#3925](https://github.com/nf-core/tools/pull/3925))
 - dockerhub action: add disk clean-up step and combine the two actions ([#3926](https://github.com/nf-core/tools/pull/3926))
-- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
 - Pin j178/prek-action action to 91fd7d7 ([#3931](https://github.com/nf-core/tools/pull/3931))
 - Simplify coverage reporting in pytest.yml ([#3934](https://github.com/nf-core/tools/pull/3934))
 - add pre-commit hook to keep uv.lock in sync ([#3933](https://github.com/nf-core/tools/pull/3933))
-- Update python:3.14-slim Docker digest to 119fd5b ([#3910](https://github.com/nf-core/tools/pull/3910))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 ([#3943](https://github.com/nf-core/tools/pull/3943))
-- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a ([#3946](https://github.com/nf-core/tools/pull/3946))
 - Fix quote handling in meta.yml ([#3948](https://github.com/nf-core/tools/pull/3948))
-- Update actions/checkout digest to 8e8c483 ([#3956](https://github.com/nf-core/tools/pull/3956))
-- Update GitHub Actions ([#3957](https://github.com/nf-core/tools/pull/3957))
-- Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
-- Update codecov/codecov-action digest to 671740a ([#3962](https://github.com/nf-core/tools/pull/3962))
 - Add support for SVG files in bump-version command ([#3978](https://github.com/nf-core/tools/pull/3978))
 - handle type for val in topics correctly ([#3991](https://github.com/nf-core/tools/pull/3991))
 - Update docker/login-action digest to c94ce9f ([#3998](https://github.com/nf-core/tools/pull/3998))
 - fix wrong parsing when output values contain spaces ([#3999](https://github.com/nf-core/tools/pull/3999))
 - fix failing devcontainer builds ([#4013](https://github.com/nf-core/tools/pull/4013))
-- Update codecov/codecov-action digest to 671740a ([#4000](https://github.com/nf-core/tools/pull/4000))
-- Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 ([#4007](https://github.com/nf-core/tools/pull/4007))
-- Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 ([#4006](https://github.com/nf-core/tools/pull/4006))
-- Update dependency textual-dev to v1.8.0 ([#4005](https://github.com/nf-core/tools/pull/4005))
-- Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 ([#4002](https://github.com/nf-core/tools/pull/4002))
-- Update dependency textual to v7 ([#4008](https://github.com/nf-core/tools/pull/4008))
-- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a29f1c ([#4009](https://github.com/nf-core/tools/pull/4009))
-- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 ([#4011](https://github.com/nf-core/tools/pull/4011))
-- Update python:3.14-slim Docker digest to 9b81fe9 ([#4012](https://github.com/nf-core/tools/pull/4012))
-
-### Template
-
-- switch to uv and prek for pipeline linting workflow ([#3942](https://github.com/nf-core/tools/pull/3942))
-- add schema to devcontainer.json ([#3908](https://github.com/nf-core/tools/pull/3908))
 
 ### Linting
 
@@ -59,6 +51,26 @@
 
 - Update to new topic version handling ([#3929](https://github.com/nf-core/tools/pull/3929))
 
+#### Version updates
+
+- Update actions/setup-python digest to 83679a8 ([#3928](https://github.com/nf-core/tools/pull/3928))
+- Update python:3.14-slim Docker digest to 119fd5b ([#3910](https://github.com/nf-core/tools/pull/3910))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.7 ([#3943](https://github.com/nf-core/tools/pull/3943))
+- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 2be0f5a ([#3946](https://github.com/nf-core/tools/pull/3946))
+- Update actions/checkout digest to 8e8c483 ([#3956](https://github.com/nf-core/tools/pull/3956))
+- Update GitHub Actions ([#3957](https://github.com/nf-core/tools/pull/3957))
+- Update astral-sh/setup-uv digest to ed21f2f ([#3959](https://github.com/nf-core/tools/pull/3959))
+- Update codecov/codecov-action digest to 671740a ([#3962](https://github.com/nf-core/tools/pull/3962))
+- Update codecov/codecov-action digest to 671740a ([#4000](https://github.com/nf-core/tools/pull/4000))
+- Update pre-commit hook pre-commit/mirrors-mypy to v1.19.1 ([#4007](https://github.com/nf-core/tools/pull/4007))
+- Update pre-commit hook astral-sh/uv-pre-commit to v0.9.28 ([#4006](https://github.com/nf-core/tools/pull/4006))
+- Update dependency textual-dev to v1.8.0 ([#4005](https://github.com/nf-core/tools/pull/4005))
+- Update mcr.microsoft.com/devcontainers/base Docker tag to v2.1.5 ([#4002](https://github.com/nf-core/tools/pull/4002))
+- Update dependency textual to v7 ([#4008](https://github.com/nf-core/tools/pull/4008))
+- Update mcr.microsoft.com/devcontainers/miniconda Docker digest to 8a29f1c ([#4009](https://github.com/nf-core/tools/pull/4009))
+- Update pre-commit hook astral-sh/ruff-pre-commit to v0.14.14 ([#4011](https://github.com/nf-core/tools/pull/4011))
+- Update python:3.14-slim Docker digest to 9b81fe9 ([#4012](https://github.com/nf-core/tools/pull/4012))
+
 ## [v3.5.1 - Terne Topi](https://github.com/nf-core/tools/releases/tag/3.5.1) - [2025-11-19]
 
 ### General

pyproject.toml

@@ -11,7 +11,7 @@ nf_core = ["**/*"]
 
 [project]
 name = "nf-core"
-version = "3.5.2"
+version = "3.6.0dev"
 description = "Helper tools for use with nf-core Nextflow pipelines."
 readme = "README.md"
 license = "MIT"