Merge branch 'dev' into get-edam-ontology

Author: mirpedrol

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.5
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -13,13 +13,13 @@ repos:
           - prettier@3.3.3
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.0.3"
+    rev: "3.1.2"
     hooks:
       - id: editorconfig-checker
         alias: ec
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.14.1"
+    rev: "v1.15.0"
     hooks:
       - id: mypy
         additional_dependencies:

CHANGELOG.md

@@ -1,17 +1,49 @@
 # nf-core/tools: Changelog
 
-## v3.2.0dev
+## v3.3.0dev
 
 ### Template
 
+- Remove the on `pull_request_target` trigger and `pull_request` types from the download test. Also drop `push` triggers on other CI tests. ([#3399](https://github.com/nf-core/tools/pull/3399))
+
 ### Linting
 
+- Add linting for ifEmpty(null) ([#3411](https://github.com/nf-core/tools/pull/3411))
+
+### Modules
+
+### Subworkflows
+
+### General
+
+- output passed to write_params_file as Path object ([#3435](https://github.com/nf-core/tools/pull/3435))
+- chore(deps): update python:3.12-slim docker digest to 69ce3ae ([#3433](https://github.com/nf-core/tools/pull/3433))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.4 ([#3438](https://github.com/nf-core/tools/pull/3438))
+- format name/value with YAML syntax ([#3442](https://github.com/nf-core/tools/pull/3442))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.5 ([#3445](https://github.com/nf-core/tools/pull/3445))
+- chore(deps): update pre-commit hook pre-commit/mirrors-mypy to v1.15.0 ([#3447](https://github.com/nf-core/tools/pull/3447))
+
+## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
+
+### Template
+
+- Remove automated release tweets ([#3419](https://github.com/nf-core/tools/pull/3419))
+- Update template components ([#3426](https://github.com/nf-core/tools/pull/3426))
+- Fix `process.shell` in `nextflow.config` ([#3416](https://github.com/nf-core/tools/pull/3416)) and split into new lines ([#3425](https://github.com/nf-core/tools/pull/3425))
+
 ### Modules
 
+- Modules created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
+
 ### Subworkflows
 
+- Subworkflows created in pipelines "local" dir now use the full template ([#3256](https://github.com/nf-core/tools/pull/3256))
+
 ### General
 
+- Update pre-commit hook editorconfig-checker/editorconfig-checker.python to v3.1.2 ([#3414](https://github.com/nf-core/tools/pull/3414))
+- Update python:3.12-slim Docker digest to 123be56 ([#3421](https://github.com/nf-core/tools/pull/3421))
+
 ## [v3.1.2 - Brass Boxfish Patch](https://github.com/nf-core/tools/releases/tag/3.1.2) - [2025-01-20]
 
 ### Template