Restructure pipeline tests and move pipeline linting into subfolder

.editorconfig

@@ -21,7 +21,7 @@ indent_style = unset
 [**/Makefile]
 indent_style = unset
 
-[tests/__snapshots__/*]
+[tests/pipelines/__snapshots__/*]
 charset = unset
 end_of_line = unset
 insert_final_newline = unset

.github/workflows/pytest.yml

@@ -67,7 +67,7 @@ jobs:
       - name: List tests
         id: list_tests
         run: |
-          echo "tests=$(find tests/test_* | tac | sed 's/tests\///g' | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
+          echo "tests=$(find tests -type f -name "test_*.py" | tac | sed 's/tests\///g'  | jq -R -s -c '{test: (split("\n")[:-1])}')" >> $GITHUB_OUTPUT
     outputs:
       tests: ${{ steps.list_tests.outputs.tests }}
 
@@ -149,10 +149,15 @@ jobs:
           name: Snapshot Report ${{ matrix.test }}
           path: ./snapshot_report.html
 
+      - name: remove slashes from test name
+        run: |
+          test=$(echo ${{ matrix.test }} | sed 's/\//__/g')
+          echo "test=${test}" >> $GITHUB_ENV
+
       - name: Upload coverage
         uses: actions/upload-artifact@65462800fd760344b1a7b4382951275a0abb4808 # v4
         with:
-          name: coverage_${{ matrix.test }}
+          name: coverage_${{ env.test }}
           path: .coverage
 
   coverage:

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
     hooks:
       - id: prettier
         additional_dependencies:
-          - prettier@3.2.5
+          - prettier@3.3.3
 
   - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
     rev: "2.7.3"

CHANGELOG.md

@@ -13,6 +13,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Rrestructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 
 ### Download