Merge pull request #60 from CCBR/precommit-fixes

fix pre-commit config

.pre-commit-config.yaml

@@ -1,11 +1,24 @@
+default_install_hook_types: [pre-commit, commit-msg]
+default_stages: [pre-commit]
+exclude: |
+  (?x)(
+      ^assets/|
+      ^docs/.*.html|
+      ^_extensions/
+   )
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
     rev: v1.2.3
     hooks:
       - id: check-added-large-files
-      #- id: check-yaml
       - id: end-of-file-fixer
       - id: trailing-whitespace
+  # spell check
+  - repo: https://github.com/codespell-project/codespell
+    rev: v2.2.4
+    hooks:
+      - id: codespell
+        # https://github.com/codespell-project/codespell/issues/1498
   # Python formatting
   - repo: https://github.com/psf/black
     rev: 23.7.0
@@ -21,13 +34,14 @@ repos:
     rev: v2.7.1
     hooks:
       - id: prettier
-  # spell check
-  - repo: https://github.com/codespell-project/codespell
-    rev: v2.2.4
-    hooks:
-      - id: codespell
   # enforce commit format
   - repo: https://github.com/compilerla/conventional-pre-commit
     rev: v2.3.0
     hooks:
       - id: conventional-pre-commit
+        stages: [commit-msg]
+        args: []
+  - repo: https://github.com/citation-file-format/cffconvert
+    rev: 054bda51dbe278b3e86f27c890e3f3ac877d616c
+    hooks:
+      - id: validate-cff

.prettierignore

@@ -0,0 +1,9 @@
+# gitignore
+.nextflow*
+work/
+data/
+results/
+.DS_Store
+*.code-workspace
+assets/*.html
+_extensions

.prettierrc

@@ -0,0 +1,4 @@
+overrides:
+    - files: "*.md"
+      options:
+          tabWidth: 2