foramatting and remove old tests

mskcc-omics-workflows · Dec 14, 2023 · 457dfc4 · 457dfc4
1 parent a35dfee
commit 457dfc4
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Showing 5 changed files with 31 additions and 54 deletions.
diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -619,7 +619,16 @@ jobs:
 
   confirm-pass:
     runs-on: ubuntu-latest
-    needs: [prettier, editorconfig, pytest-changes, nf-core-lint, pytest, nf-test-changes, nf-test]
+    needs:
+      [
+        prettier,
+        editorconfig,
+        pytest-changes,
+        nf-core-lint,
+        pytest,
+        nf-test-changes,
+        nf-test,
+      ]
     if: always()
     steps:
       - name: All tests ok

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
@@ -0,0 +1,21 @@
+repos:
+  - repo: https://github.com/pre-commit/mirrors-prettier
+    rev: "v3.0.3"
+    hooks:
+      - id: prettier
+  - repo: https://github.com/python-jsonschema/check-jsonschema
+    rev: 0.27.0
+    hooks:
+      - id: check-jsonschema
+        # match meta.ymls in one of the subdirectories of modules/nf-core
+        files: ^modules/nf-core/.*/meta\.yml$
+        args: ["--schemafile", "modules/yaml-schema.json"]
+      - id: check-jsonschema
+        # match meta.ymls in one of the subdirectories of subworkflows/nf-core
+        files: ^subworkflows/nf-core/.*/meta\.yml$
+        args: ["--schemafile", "subworkflows/yaml-schema.json"]
+      - id: check-github-workflows
+  - repo: https://github.com/renovatebot/pre-commit-hooks
+    rev: 37.43.4
+    hooks:
+      - id: renovate-config-validator
diff --git a/tests/modules/msk/gbcms/main.nf b/tests/modules/msk/gbcms/main.nf
diff --git a/tests/modules/msk/gbcms/nextflow.config b/tests/modules/msk/gbcms/nextflow.config
diff --git a/tests/modules/msk/gbcms/test.yml b/tests/modules/msk/gbcms/test.yml