make CLI startup faster

.pre-commit-config.yaml

@@ -4,6 +4,7 @@ repos:
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
+        priority: 10
       - id: ruff-format # formatter
   - repo: https://github.com/pre-commit/mirrors-prettier
     rev: "v3.1.0"
@@ -17,6 +18,7 @@ repos:
     hooks:
       - id: trailing-whitespace
         args: [--markdown-linebreak-ext=md]
+        priority: 10
         exclude: |
           (?x)^(
               .*\.snap$|
@@ -25,6 +27,7 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
       - id: end-of-file-fixer
+        priority: 10
         exclude: |
           (?x)^(
               .*\.snap$|
@@ -37,6 +40,7 @@ repos:
     hooks:
       - id: mypy
         args: [--ignore-missing-imports, --scripts-are-modules, -n4]
+        priority: 20
         additional_dependencies:
           - types-PyYAML
           - types-requests
@@ -48,10 +52,12 @@ repos:
     rev: 0.11.19
     hooks:
       - id: uv-lock
+        priority: 20
   - repo: local
     hooks:
       - id: lint-test-docstrings
         name: Check lint test names are documented in docstrings
         language: system
         entry: python3 docs/api/check_lint_docstrings.py
+        priority: 20
         files: ^nf_core/(modules|subworkflows)/lint/.*\.py$

CHANGELOG.md

@@ -4,12 +4,11 @@
 
 ### General
 
-- Update pre-commit hook pre-commit/mirrors-mypy to v2 ([#4270](https://github.com/nf-core/tools/pull/4270))
 - container configs: use correct key for conda configs ([#4269](https://github.com/nf-core/tools/pull/4269))
 - Coerce launch params_out to Path to fix AttributeError (#4299) ([#4317](https://github.com/nf-core/tools/pull/4317))
 - generate valid Markdown when piping schema docs to file ([#4319](https://github.com/nf-core/tools/pull/4319))
 - fix API docs bug in pydantic autodoc ([#4320](https://github.com/nf-core/tools/pull/4320))
-- Update pre-commit npm dependencies to v3.8.4 ([#4335](https://github.com/nf-core/tools/pull/4335))
+- Improve CLI startup speed ([#4383](https://github.com/nf-core/tools/pull/4383))
 
 ### Linting
 
@@ -21,12 +20,10 @@
 ### Modules
 
 - `modules info`: handle one element channels correctly ([#4268](https://github.com/nf-core/tools/pull/4268))
-- feat: module lint for module name granularity ([#4325](https://github.com/nf-core/tools/pull/4325))
+- `module` lint for module name matching against nf-core module naming specifications ([#4325](https://github.com/nf-core/tools/pull/4325))
 - Clarify execution context of nf-core modules test command ([#4346](https://github.com/nf-core/tools/pull/4346))
 - Add `nf-core modules containers create` to build module containers via Seqera Wave and record them in the `containers:` section of `meta.yml` ([#3954](https://github.com/nf-core/tools/pull/3954))
-- Container linting now validates the `containers:` section of `meta.yml` (Wave modules). The legacy `main.nf` container checks (URL reachability, registry prefix, docker/singularity tag match) have been removed; modules still using the old container syntax get a `deprecated_container_syntax` warning instead ([#3954](https://github.com/nf-core/tools/pull/3954))
-
-### Subworkflows
+- Add a log hint in `modules create` for `create containers` and switch `modules bump-versions` to use Seqera containers ([#4374](https://github.com/nf-core/tools/pull/4374))
 
 ### Template
 
@@ -45,6 +42,9 @@
 
 #### Version updates
 
+- Update pre-commit hook pre-commit/mirrors-mypy to v2 ([#4270](https://github.com/nf-core/tools/pull/4270))
+- Update pre-commit npm dependencies to v3.8.4 ([#4335](https://github.com/nf-core/tools/pull/4335))
+
 ## [v4.0.2 - Bold Boa Patch 2](https://github.com/nf-core/tools/releases/tag/4.0.2) - [2026-04-30]
 
 ### General