Merge branch 'dev' into nicer-lint-bot-comment

CHANGELOG.md

@@ -13,6 +13,7 @@
 - Remove `nfcore_external_java_deps.jar` from lib directory in pipeline template ([#2675](https://github.com/nf-core/tools/pull/2675))
 - Add function to check `-profile` is well formatted ([#2678](https://github.com/nf-core/tools/pull/2678))
 - Add new pipeline error message pointing to docs when 'requirement exceeds available memory' error message ([#2680](https://github.com/nf-core/tools/pull/2680))
+- add 👀👍🏻🎉😕 reactions to fix-linting-bot action ([#2692](https://github.com/nf-core/tools/pull/2692))
 
 ### Download
 
@@ -21,7 +22,8 @@
 - Fix linting of a pipeline with patched custom module ([#2669](https://github.com/nf-core/tools/pull/2669))
 - linting a pipeline also lints the installed subworkflows ([#2677](https://github.com/nf-core/tools/pull/2677))
 - environment.yml name must be lowercase ([#2676](https://github.com/nf-core/tools/pull/2676))
-- template: add 👀👍🏻🎉😕 reactions to fix-bot action ([#2692](https://github.com/nf-core/tools/pull/2692))
+- lint `nextflow.config` default values match the ones specified in `nextflow_schema.json` ([#2684](https://github.com/nf-core/tools/pull/2684))
+
 
 ### Modules
 

nf_core/lint/nextflow_config.py

@@ -1,6 +1,9 @@
 import logging
 import os
 import re
+from pathlib import Path
+
+from nf_core.schema import PipelineSchema
 
 log = logging.getLogger(__name__)
 
@@ -113,6 +116,18 @@ def nextflow_config(self):
 
     * A ``test`` configuration profile should exist.
 
+    **The default values in ``nextflow.config`` should match the default values defined in the ``nextflow_schema.json``.**
+
+    .. tip:: You can choose to ignore tests for the default value of an specific parameter
+             by creating a file called ``.nf-core.yml`` in the root of your pipeline and creating
+             a list the config parameters that should be ignored. For example to ignore the default value for the input parameter:
+
+             .. code-block:: yaml
+
+                lint:
+                    nextflow_config:
+                        - config_defaults:
+                            - params.input
     """
     passed = []
     warned = []
@@ -347,4 +362,40 @@ def nextflow_config(self):
             else:
                 failed.append("nextflow.config does not contain configuration profile `test`")
 
+    # Check that the default values in nextflow.config match the default values defined in the nextflow_schema.json
+    ignore_defaults = []
+    for item in ignore_configs:
+        if isinstance(item, dict) and "config_defaults" in item:
+            ignore_defaults = item.get("config_defaults", [])
+    schema_path = Path(self.wf_path) / "nextflow_schema.json"
+    schema = PipelineSchema()
+    schema.schema_filename = schema_path
+    schema.no_prompts = True
+    schema.load_schema()
+    schema.get_schema_defaults()  # Get default values from schema
+    self.nf_config.keys()  # Params in nextflow.config
+    for param_name in schema.schema_defaults.keys():
+        param = "params." + param_name
+        # Convert booleans to strings if needed
+        schema_default = (
+            "true"
+            if str(schema.schema_defaults[param_name]) == "True"
+            else "false"
+            if str(schema.schema_defaults[param_name]) == "False"
+            else str(schema.schema_defaults[param_name])
+        )
+        if param in ignore_defaults:
+            ignored.append(f"Config default ignored: {param}")
+        elif param in self.nf_config.keys():
+            if str(self.nf_config[param]) == schema_default:
+                passed.append(f"Config default value correct: {param}")
+            else:
+                failed.append(
+                    f"Config default value incorrect: `{param}` is set as {self._wrap_quotes(schema_default)} in `nextflow_schema.json` but is {self._wrap_quotes(self.nf_config[param])} in `nextflow.config`."
+                )
+        else:
+            failed.append(
+                f"Default value from the Nextflow schema '{param} = {self._wrap_quotes(schema_default)}' not found in `nextflow.config`."
+            )
+
     return {"passed": passed, "warned": warned, "failed": failed, "ignored": ignored}

tests/lint/nextflow_config.py

@@ -1,5 +1,6 @@
 import os
 import re
+from pathlib import Path
 
 import nf_core.create
 import nf_core.lint
@@ -53,3 +54,66 @@ def test_nextflow_config_missing_test_profile_failed(self):
     result = lint_obj.nextflow_config()
     assert len(result["failed"]) > 0
     assert len(result["warned"]) == 0
+
+
+def test_default_values_match(self):
+    """Test that the default values in nextflow.config match the default values defined in the nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["warned"]) == 0
+    assert "Config default value correct: params.max_cpus" in result["passed"]
+    assert "Config default value correct: params.validate_params" in result["passed"]
+
+
+def test_default_values_fail(self):
+    """Test linting fails if the default values in nextflow.config do not match the ones defined in the nextflow_schema.json."""
+    new_pipeline = self._make_pipeline_copy()
+    # Change the default value of max_cpus in nextflow.config
+    nf_conf_file = Path(new_pipeline) / "nextflow.config"
+    with open(nf_conf_file) as f:
+        content = f.read()
+        fail_content = re.sub(r"\bmax_cpus                   = 16\b", "max_cpus                   = 0", content)
+    with open(nf_conf_file, "w") as f:
+        f.write(fail_content)
+    # Change the default value of max_memory in nextflow_schema.json
+    nf_schema_file = Path(new_pipeline) / "nextflow_schema.json"
+    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)
+    lint_obj._load_pipeline_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 2
+    assert (
+        "Config default value incorrect: `params.max_cpus` is set as `16` in `nextflow_schema.json` but is `0` in `nextflow.config`."
+        in result["failed"]
+    )
+    assert (
+        "Config default value incorrect: `params.max_memory` is set as `18.GB` in `nextflow_schema.json` but is `128.GB` in `nextflow.config`."
+        in result["failed"]
+    )
+
+
+def test_default_values_ignored(self):
+    """Test ignoring linting of default values."""
+    new_pipeline = self._make_pipeline_copy()
+    # Add max_cpus to the ignore list
+    nf_core_yml = Path(new_pipeline) / ".nf-core.yml"
+    with open(nf_core_yml, "w") as f:
+        f.write(
+            "repository_type: pipeline\nlint:\n  nextflow_config:\n    - config_defaults:\n      - params.max_cpus\n"
+        )
+    lint_obj = nf_core.lint.PipelineLint(new_pipeline)
+    lint_obj._load_pipeline_config()
+    lint_obj._load_lint_config()
+    result = lint_obj.nextflow_config()
+    assert len(result["failed"]) == 0
+    assert len(result["ignored"]) == 1
+    assert "Config default value correct: params.max_cpus" not in result["passed"]
+    assert "Config default ignored: params.max_cpus" in result["ignored"]

tests/test_lint.py

@@ -219,6 +219,9 @@ def test_sphinx_md_files(self):
         test_multiqc_incorrect_export_plots,
     )
     from .lint.nextflow_config import (  # type: ignore[misc]
+        test_default_values_fail,
+        test_default_values_ignored,
+        test_default_values_match,
         test_nextflow_config_bad_name_fail,
         test_nextflow_config_dev_in_release_mode_failed,
         test_nextflow_config_example_pass,