Merge branch 'dev' into renovate/pytest-textual-snapshot-1.x

.github/workflows/pytest.yml

@@ -75,8 +75,8 @@ jobs:
     name: Run ${{matrix.test}} with Python ${{ needs.setup.outputs.python-version }} on ${{ needs.setup.outputs.runner }}
     needs: [setup, list_tests]
     if: ${{ needs.setup.outputs.run-tests }}
-    # run on self-hosted runners for test_components.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
-    runs-on: ${{ matrix.test == 'test_components.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
+    # run on self-hosted runners for test_components_generate_snapshot.py (because of the gitlab branch), based on the input if it is dispatched manually, on github if it is a rerun or on self-hosted by default
+    runs-on: ${{ matrix.test == 'components/test_components_generate_snapshot.py' && 'self-hosted' || (github.event.inputs.runners || github.run_number > 1 && 'ubuntu-latest' || 'self-hosted') }}
     strategy:
       matrix: ${{ fromJson(needs.list_tests.outputs.tests) }}
       fail-fast: false # run all tests even if one fails

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.3
+    rev: v0.9.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -10,16 +10,29 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - [email protected]
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.1.2"
+          - [email protected]
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v5.0.0
     hooks:
-      - id: editorconfig-checker
-        alias: ec
-
+      - id: trailing-whitespace
+        args: [--markdown-linebreak-ext=md]
+        exclude: |
+          (?x)^(
+              .*\.snap$|
+              nf_core/pipeline-template/subworkflows/.*|
+              nf_core/pipeline-template/modules/.*|
+              tests/pipelines/__snapshots__/.*
+          )$
+      - id: end-of-file-fixer
+        exclude: |
+          (?x)^(
+              .*\.snap$|
+              nf_core/pipeline-template/subworkflows/.*|
+              nf_core/pipeline-template/modules/.*|
+              tests/pipelines/__snapshots__/.*
+          )$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v1.14.1"
+    rev: "v1.15.0"
     hooks:
       - id: mypy
         additional_dependencies:

.prettierignore

@@ -12,4 +12,3 @@ tests/data/pipeline_create_template_skip.yml
 # don't run on things handled by ruff
 *.py
 *.pyc
-

.prettierrc.yml

@@ -1 +1,6 @@
 printWidth: 120
+tabWidth: 4
+overrides:
+  - files: "*.{md,yml,yaml,html,css,scss,js,cff}"
+    options:
+      tabWidth: 2

CHANGELOG.md

@@ -5,20 +5,40 @@
 ### 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))
+- Add nf-core template version badges to README ([#3396](https://github.com/nf-core/tools/pull/3396))
+- Add Bluesky badge to readme ([#3475](https://github.com/nf-core/tools/pull/3475))
 
 ### Linting
 
 - Add linting for ifEmpty(null) ([#3411](https://github.com/nf-core/tools/pull/3411))
+- Fix arbitrarily nested params schema linting ([#3443](https://github.com/nf-core/tools/pull/3443))
+- fix: linting with comments after the input directive ([#3458](https://github.com/nf-core/tools/pull/3458))
+- EDAM ontology fixes ([#3460](https://github.com/nf-core/tools/pull/3460))
 
 ### Modules
 
+- increase meta index for multiple input channels ([#3463](https://github.com/nf-core/tools/pull/3463))
+
 ### 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 dependency pytest-textual-snapshot to v1.1.0 ([#3439](https://github.com/nf-core/tools/pull/3439))
+- 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 editorconfig-checker/editorconfig-checker.python to v3.2.0 ([#3446](https://github.com/nf-core/tools/pull/3446))
+- 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))
+- Update prettier to 3.5.0 ([#3448](https://github.com/nf-core/tools/pull/3448))
+- chore(deps): update python:3.12-slim docker digest to 34656cd ([#3450](https://github.com/nf-core/tools/pull/3450))
+- Remove Twitter from README ([#3454](https://github.com/nf-core/tools/pull/3454))
+- docs: fix contributing link in the main README ([#3459](https://github.com/nf-core/tools/pull/3459))
+- Cleanup: Removed Redundant if Condition ([#3468](https://github.com/nf-core/tools/pull/3468))
+- chore(deps): update gitpod/workspace-base docker digest to 7f35e40 ([#3473](https://github.com/nf-core/tools/pull/3473))
+- chore(deps): update python:3.12-slim docker digest to aaa3f8c ([#3474](https://github.com/nf-core/tools/pull/3474))
+- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.9.9 ([#3470](https://github.com/nf-core/tools/pull/3470))
 
 ## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]
 
@@ -71,7 +91,7 @@
 - Use outputs instead of the environment to pass around values between steps in the Download Test Action ([#3351](https://github.com/nf-core/tools/pull/3351))
 - Fix pre commit template ([#3358](https://github.com/nf-core/tools/pull/3358))
 - Set LICENSE copyright to nf-core community ([#3366](https://github.com/nf-core/tools/pull/3366))
-- fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
+- Fix including modules.config ([#3356](https://github.com/nf-core/tools/pull/3356))
 
 ### Linting
 

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:69ce3aed05675d284bee807e7c45e560e98db21fb1e4c670252b4ee0f2496b6d
+FROM python:3.12-slim@sha256:aaa3f8cb64dd64e5f8cb6e58346bdcfa410a108324b0f28f1a7cc5964355b211
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

README.md

@@ -61,7 +61,7 @@ pip install --upgrade -r requirements-dev.txt -e .
 
 ## Contributions and Support
 
-If you would like to contribute to this package, please see the [contributing guidelines](.github/CONTRIBUTING.md).
+If you would like to contribute to this package, please see the [contributing guidelines](CONTRIBUTING.md).
 
 For further information or help, don't hesitate to get in touch on the [Slack `#tools` channel](https://nfcore.slack.com/channels/tools) (you can join with [this invite](https://nf-co.re/join/slack)).