Add tests for assignment and referencing of params in main.nf

CHANGELOG.md

@@ -21,7 +21,8 @@
 - Update GitHub Actions ([#2827](https://github.com/nf-core/tools/pull/2827))
 - Switch to setup-nf-test ([#2834](https://github.com/nf-core/tools/pull/2834))
 - Update pre-commit hook astral-sh/ruff-pre-commit to v0.3.2 ([#2836](https://github.com/nf-core/tools/pull/2836))
-- optimize layers in dockerfile ([#2842](https://github.com/nf-core/tools/pull/2842))
+- Add tests for assignment and referencing of params in main.nf ([#2841](https://github.com/nf-core/tools/pull/2841))
+- Optimize layers in dockerfile ([#2842](https://github.com/nf-core/tools/pull/2842))
 - Update gitpod/workspace-base Docker digest to 1e133e5 ([#2843](https://github.com/nf-core/tools/pull/2843))
 
 ## [v2.13.1 - Tin Puppy Patch](https://github.com/nf-core/tools/releases/tag/2.13) - [2024-02-29]

nf_core/lint/nextflow_config.py

@@ -374,7 +374,6 @@ def nextflow_config(self):
     schema.load_schema()
     schema.get_schema_defaults()  # Get default values from schema
     schema.get_schema_types()  # Get types from schema
-    self.nf_config.keys()  # Params in nextflow.config
     for param_name in schema.schema_defaults.keys():
         param = "params." + param_name
         if param in ignore_defaults:

tests/lint/nextflow_config.py

@@ -83,7 +83,6 @@ def test_default_values_fail(self):
     with open(nf_schema_file) as f:
         content = f.read()
         fail_content = re.sub(r'"default": "128.GB"', '"default": "18.GB"', content)
-        print(fail_content)
     with open(nf_schema_file, "w") as f:
         f.write(fail_content)
     lint_obj = nf_core.lint.PipelineLint(new_pipeline)
@@ -100,6 +99,36 @@ def test_default_values_fail(self):
     )
 
 
+def test_catch_params_assignment_in_main_nf(self):
+    """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add parameter assignment in main.nf
+    main_nf_file = Path(new_pipeline) / "main.nf"
+    with open(main_nf_file, "a") as f:
+        f.write("params.max_time = 42")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 1
+    assert (
+        result["failed"][0]
+        == "Config default value incorrect: `params.max_time` is set as `240.h` in `nextflow_schema.json` but is `null` in `nextflow.config`."
+    )
+
+
+def test_allow_params_reference_in_main_nf(self):
+    """Test linting allows for references like `params.aligner == 'bwa'` in main.nf. The test will detect if the bug mentioned in GitHub-issue #2833 reemerges."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add parameter reference in main.nf
+    main_nf_file = Path(new_pipeline) / "main.nf"
+    with open(main_nf_file, "a") as f:
+        f.write("params.max_time == 42")
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+
+
 def test_default_values_ignored(self):
     """Test ignoring linting of default values."""
     new_pipeline = self._make_pipeline_copy()

tests/test_lint.py

@@ -221,6 +221,8 @@ def test_sphinx_md_files(self):
         test_multiqc_incorrect_export_plots,
     )
     from .lint.nextflow_config import (  # type: ignore[misc]
+        test_allow_params_reference_in_main_nf,
+        test_catch_params_assignment_in_main_nf,
         test_default_values_fail,
         test_default_values_float,
         test_default_values_float_fail,