refactor according to review

Clinical-Genomics · Jan 17, 2025 · 99403ea · 99403ea
1 parent 659e9e8
commit 99403ea
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Showing 2 changed files with 7 additions and 7 deletions.
diff --git a/tests/cli/workflow/nf_analysis/test_cli_run.py b/tests/cli/workflow/nf_analysis/test_cli_run.py
@@ -137,7 +137,7 @@ def test_run_case_from_start_dry_run(
     case_id: str = request.getfixturevalue(f"{workflow}_case_id")
 
     # GIVEN mocked config files
-    request.getfixturevalue(f"{workflow}_mock_config")
+    request.getfixturevalue(f"{workflow}_config")
 
     # WHEN invoking a command with dry-run specified
     result = cli_runner.invoke(
@@ -171,7 +171,7 @@ def test_run_case_with_revision_dry_run(
     case_id: str = request.getfixturevalue(f"{workflow}_case_id")
 
     # GIVEN a mocked config
-    request.getfixturevalue(f"{workflow}_mock_config")
+    request.getfixturevalue(f"{workflow}_config")
 
     # WHEN invoking a command with dry-run and revision specified
     result = cli_runner.invoke(

diff --git a/tests/conftest.py b/tests/conftest.py
@@ -2604,8 +2604,8 @@ def nallo_dir(tmpdir_factory, apps_dir: Path) -> str:
 
 
 @pytest.fixture(scope="function")
-def nallo_mock_config(nallo_dir: Path, nallo_case_id: str) -> None:
-    """Create nallo samplesheet.csv file for testing"""
+def nallo_config(nallo_dir: Path, nallo_case_id: str) -> None:
+    """Create Nallo samplesheet.csv file for testing"""
     Path.mkdir(Path(nallo_dir, nallo_case_id), parents=True, exist_ok=True)
     Path(nallo_dir, nallo_case_id, f"{nallo_case_id}_samplesheet").with_suffix(
         FileExtensions.CSV
@@ -2921,7 +2921,7 @@ def mock_deliverable(
 
 
 @pytest.fixture(scope="function")
-def raredisease_mock_config(raredisease_dir: Path, raredisease_case_id: str) -> None:
+def raredisease_config(raredisease_dir: Path, raredisease_case_id: str) -> None:
     """Create samplesheet.csv file for testing"""
     Path.mkdir(Path(raredisease_dir, raredisease_case_id), parents=True, exist_ok=True)
     Path(raredisease_dir, raredisease_case_id, f"{raredisease_case_id}_samplesheet").with_suffix(
@@ -3443,7 +3443,7 @@ def rnafusion_mock_analysis_finish(
 
 
 @pytest.fixture(scope="function")
-def rnafusion_mock_config(rnafusion_dir: Path, rnafusion_case_id: str) -> None:
+def rnafusion_config(rnafusion_dir: Path, rnafusion_case_id: str) -> None:
     """Create samplesheet.csv file for testing"""
     Path.mkdir(Path(rnafusion_dir, rnafusion_case_id), parents=True, exist_ok=True)
     Path(rnafusion_dir, rnafusion_case_id, f"{rnafusion_case_id}_samplesheet.csv").with_suffix(
@@ -3496,7 +3496,7 @@ def tomte_gene_panel_path(tomte_dir, tomte_case_id) -> Path:
 
 
 @pytest.fixture(scope="function")
-def tomte_mock_config(tomte_dir: Path, tomte_case_id: str) -> None:
+def tomte_config(tomte_dir: Path, tomte_case_id: str) -> None:
     """Create Tomte samplesheet.csv file for testing."""
     Path.mkdir(Path(tomte_dir, tomte_case_id), parents=True, exist_ok=True)
     Path(tomte_dir, tomte_case_id, f"{tomte_case_id}_samplesheet").with_suffix(