Merge branch 'dev' into bump-version-nf-snap

Author: mashehu

.editorconfig

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.9.5
+    rev: v0.9.9
     hooks:
       - id: ruff # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -11,13 +11,26 @@ repos:
       - id: prettier
         additional_dependencies:
           - [email protected]
-
-  - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
-    rev: "3.2.0"
+  - 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: "v1.15.0"
     hooks:

.github/workflows/update_components_template.yml

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

.pre-commit-config.yaml

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

.prettierignore

@@ -6,6 +6,7 @@
 
 - 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
 
@@ -33,6 +34,10 @@
 - 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]
 

.prettierrc.yml

@@ -1,4 +1,4 @@
-FROM python:3.12-slim@sha256:34656cd90456349040784165b9decccbcee4de66f3ead0a1168ba893455afd1e
+FROM python:3.12-slim@sha256:aaa3f8cb64dd64e5f8cb6e58346bdcfa410a108324b0f28f1a7cc5964355b211
 LABEL authors="[email protected],[email protected]" \
     description="Docker image containing requirements for nf-core/tools"
 

CHANGELOG.md

@@ -2,7 +2,7 @@
 #   docker build -t gitpod:test -f nf_core/gitpod/gitpod.Dockerfile .
 
 # See https://docs.renovatebot.com/docker/#digest-pinning for why a digest is used.
-FROM gitpod/workspace-base@sha256:12853f7c901eb2b677a549cb112c85f9679d18feb30093bcc63aa252540ecad9
+FROM gitpod/workspace-base@sha256:7f35e401405c38ebc1185dfc3d6c066f73a524e8b86641453ea4690cc5c24fb6
 
 USER root
 

Dockerfile

@@ -18,8 +18,6 @@ concurrency:
 jobs:
   test:
     name: "Run pipeline with test data (${{ matrix.NXF_VER }} | ${{ matrix.test_name }} | ${{ matrix.profile }})"
-    # Only run on push if this is the nf-core dev branch (merged PRs)
-    if: "${{{% endraw %} github.event_name != 'push' || (github.event_name == 'push' && github.repository == '{{ name }}') {% raw %}}}"
     runs-on: ubuntu-latest
     strategy:
       matrix:

nf_core/assets/logo/placeholder_logo.svg

@@ -11,7 +11,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Download lint results
-        uses: dawidd6/action-download-artifact@20319c5641d495c8a52e688b7dc5fada6c3a9fbc # v8
+        uses: dawidd6/action-download-artifact@07ab29fd4a977ae4d2b275087cf67563dfdf0295 # v9
         with:
           workflow: linting.yml
           workflow_conclusion: completed