This release contains some template changes and nf-core/tools updates.

🌟 Highlights 🌟

nf-core/tools functionalities

We included a new linting test to ensure that nf-test snapshots contain the versions.yml file.
Components (modules and subworkflows) can now handle more possible git URLs (ssh:// and ftp://).
The nf-core download command has a new argument --tag, which allows adding additional tags to select particular revisions in the Seqera Platform interface. For example, --tag "3.10=validated"{:bash} would allow you to quickly select the validated version of the pipeline.

We updated the GitHub Action which tests that the pipeline can be downloaded correctly (download_pipeline.yml)
We removed pyproject.toml from the template.
Pipeline-specific institutional configs support is now activated for all pipelines by default.
The .nf-core.yml file contains now the version of the pipeline template.

Remove fasta default from nextflow.config (#2828)
Update templates to use nf-core/setup-nextflow v2 (#2818)
Link to troubleshooting docs when pipeline fails (#2845)
Add fallback to download_pipeline.yml in case the pipeline does not support stub runs (#2846)
Set topic variable correctly in the mastodon announcement (#2848)
Add a cleanup action to download_pipeline.yml to fix failures caused by inadequate storage space on the runner (#2849)
Update python to 3.12 (#2805)
Remove pyproject.toml from template root
Shorten lines in pipeline template (#2908)
Add a new hidden --pipelines_testdata_base_path parameter to more easily switch locations of test data in test configs (#2931)[https://github.com//pull/2931]
Permanently activated pipeline-specific institutional configs support for all pipelines without need for manual intervention (#2936)
Template config: conda.channels, not channels (#2950)
Handles multiple DOIs + doi.org resolver from manifest.doi (#2946)
Update included components (#2949)
Update .editorconfig (#2953)

Only match assignments of params in main.nf and not references like params.aligner == <something> (#2833)
Include test for presence of versions in snapshot (#2888)
Components: set correct sha before running component lint tests (#2952)
Less strict logo comparison (#2956)
Handle request errors more gracefully for actions validation (#2959)

Replace --tower with --platform. The former will remain for backwards compatability for now but will be removed in a future release. (#2853)
Better error message when GITHUB_TOKEN exists but is wrong/outdated
New --tag argument to add custom tags during a pipeline download (#2938)

Handle more complete list of possible git URL forms (ssh:// and ftp:// prefixes specifically) (#2945)
Fix path in component update script (#2823)

Update CI to use nf-core/setup-nextflow v2 (#2819)
Changelog bot: handle also patch version before dev suffix (#2820)
Add force_pr flag to sync, to force a PR even though there are no changes committed (#2822)
Update prettier to 3.2.5 (#2830)
Update GitHub Actions (#2827), (#2902), (#2927), (#2939)
Switch to setup-nf-test (#2834)
Add tests for assignment and referencing of params in main.nf (#2841)
Optimize layers in dockerfile (#2842)
Update python:3.11-slim Docker digest to a2eb07f (#2847)
Strip out mention of "Nextflow Tower" and replace with "Seqera Platform" wherever possible
Fix issue with config resolution that was causing nested configs to behave unexpectedly (#2862)
Fix schema docs console output truncating (#2880)
Ensure path object converted to string before stripping quotes (#2878)
Fix incorrect assertions for called_with on mocks (#2891)
Make cli-provided module/subworkflow names case insensitive (#2869)
Get immediate parent path name for schema creation (#2886)
Remove old references to CUSTOMDUMPSOFTWAREVERSIONS and add linting checks (#2897)
Update pre-commit hook pre-commit/mirrors-mypy to v1.10.0 (#2933)
Update codecov/codecov-action digest to 5ecb98a (#2948)
Update gitpod/workspace-base Docker digest to 124f2b8 (#2943)
fix(collectfile): sort true for methods_description_mqc.yaml (#2947)
chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.4.3 (#2951)
Restructure CHANGELOG.md (#2954)