Removes all remaining references to max_* params

.github/workflows/create-test-wf.yml

@@ -75,7 +75,7 @@ jobs:
           pwd
           # echo content of current directory
           ls -la
-          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results --max_cpus 4
+          nextflow run nf-core-testpipeline -profile test,self_hosted_runner --outdir ./results
 
       - name: Upload log file artifact
         if: ${{ always() }}

CHANGELOG.md

@@ -37,6 +37,7 @@
 - add option to exclude test configs from pipeline template ([#3133](https://github.com/nf-core/tools/pull/3133))
 - add option to exclude tower.yml from pipeline template ([#3134](https://github.com/nf-core/tools/pull/3134))
 - Add tests to ensure all files are part of a template customisation group and all groups are tested ([#3099](https://github.com/nf-core/tools/pull/3099))
+- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 
 ### Linting
 
@@ -98,7 +99,6 @@
 
 - Don't cache pip in `linting.yml` ([#2961](https://github.com/nf-core/tools/pull/2961))
 - Lint pipelines with the nf-core template version and post comment if it is outdated ([#2978](https://github.com/nf-core/tools/pull/2978))
-- Replaces the old custom `check_max()` function with the Nextflow native `resourceLimits` directive ([#3037](https://github.com/nf-core/tools/pull/3037))
 
 ### General
 

nf_core/pipelines/lint/nextflow_config.py

@@ -80,7 +80,7 @@ def nextflow_config(self) -> Dict[str, List[str]]:
     * ``params.nf_required_version``: The old method for specifying the minimum Nextflow version. Replaced by ``manifest.nextflowVersion``
     * ``params.container``: The old method for specifying the dockerhub container address. Replaced by ``process.container``
     * ``igenomesIgnore``: Changed to ``igenomes_ignore``
-    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive.
+    * ``params.max_cpus``: Old method of specifying the maximum number of CPUs a process can request. Replaced by native Nextflow `resourceLimits`directive in config files.
     * ``params.max_memory``: Old method of specifying the maximum number of memory can request. Replaced by native Nextflow `resourceLimits`directive.
     * ``params.max_time``: Old method of specifying the maximum number of CPUs can request. Replaced by native Nextflow `resourceLimits`directive.
 
@@ -149,7 +149,13 @@ def nextflow_config(self) -> Dict[str, List[str]]:
         ["params.input"],
     ]
     # Throw a warning if these are missing
-    config_warn = [["manifest.mainScript"], ["timeline.file"], ["trace.file"], ["report.file"], ["dag.file"]]
+    config_warn = [
+        ["manifest.mainScript"],
+        ["timeline.file"],
+        ["trace.file"],
+        ["report.file"],
+        ["dag.file"],
+    ]
     # Old depreciated vars - fail if present
     config_fail_ifdefined = [
         "params.nf_required_version",
@@ -207,7 +213,11 @@ def nextflow_config(self) -> Dict[str, List[str]]:
             )
 
     # Remove field that should be ignored according to the linting config
-    ignore_configs = self.lint_config.get("nextflow_config", []) if self.lint_config is not None else []
+    ignore_configs = (
+        self.lint_config.get("nextflow_config", [])
+        if self.lint_config is not None
+        else []
+    )
 
     for cfs in config_fail:
         for cf in cfs:

tests/pipelines/lint/test_nextflow_config.py

@@ -30,8 +30,9 @@ def test_default_values_match(self):
         result = lint_obj.nextflow_config()
         assert len(result["failed"]) == 0
         assert len(result["warned"]) == 0
-        assert "Config default value correct: params.max_cpus" in str(result["passed"])
-        assert "Config default value correct: params.validate_params" in str(result["passed"])
+        assert "Config default value correct: params.validate_params" in str(
+            result["passed"]
+        )
 
     def test_nextflow_config_bad_name_fail(self):
         """Tests that config variable existence test fails with bad pipeline name"""
@@ -69,88 +70,16 @@ def test_nextflow_config_missing_test_profile_failed(self):
         assert len(result["failed"]) > 0
         assert len(result["warned"]) == 0
 
-    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."""
-        # Change the default value of max_cpus in nextflow.config
-        nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
-        with open(nf_conf_file) as f:
-            content = f.read()
-            fail_content = re.sub(r"\bmax_cpus\s*=\s*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(self.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)
-        with open(nf_schema_file, "w") as f:
-            f.write(fail_content)
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.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_catch_params_assignment_in_main_nf(self):
-        """Test linting fails if main.nf contains an assignment to a parameter from nextflow_schema.json."""
-        # Add parameter assignment in main.nf
-        main_nf_file = Path(self.new_pipeline) / "main.nf"
-        with open(main_nf_file, "a") as f:
-            f.write("params.max_time = 42")
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.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."""
-        # Add parameter reference in main.nf
-        main_nf_file = Path(self.new_pipeline) / "main.nf"
-        with open(main_nf_file, "a") as f:
-            f.write("params.max_time == 42")
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.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."""
-        # Add max_cpus to the ignore list
-        nf_core_yml_path = Path(self.new_pipeline) / ".nf-core.yml"
-        nf_core_yml = NFCoreYamlConfig(
-            repository_type="pipeline", lint={"nextflow_config": [{"config_defaults": ["params.max_cpus"]}]}
-        )
-        with open(nf_core_yml_path, "w") as f:
-            yaml.dump(nf_core_yml.model_dump(), f)
-
-        lint_obj = nf_core.pipelines.lint.PipelineLint(self.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_cpu" not in str(result["passed"])
-        assert "Config default ignored: params.max_cpus" in str(result["ignored"])
-
     def test_default_values_float(self):
         """Test comparing two float values."""
         # Add a float value `dummy=0.0001` to the nextflow.config below `validate_params`
         nf_conf_file = Path(self.new_pipeline) / "nextflow.config"
         with open(nf_conf_file) as f:
             content = f.read()
             fail_content = re.sub(
-                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+                r"validate_params\s*=\s*true",
+                "params.validate_params = true\ndummy = 0.000000001",
+                content,
             )
         with open(nf_conf_file, "w") as f:
             f.write(fail_content)
@@ -180,7 +109,9 @@ def test_default_values_float_fail(self):
         with open(nf_conf_file) as f:
             content = f.read()
             fail_content = re.sub(
-                r"validate_params\s*=\s*true", "params.validate_params = true\ndummy = 0.000000001", content
+                r"validate_params\s*=\s*true",
+                "params.validate_params = true\ndummy = 0.000000001",
+                content,
             )
         with open(nf_conf_file, "w") as f:
             f.write(fail_content)