remove resourceLimits from nf-test nextflow.config file and use profile instead

Author: mirpedrol

nf_core/pipeline-template/tests/nextflow.config

@@ -9,12 +9,4 @@
 params.modules_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/modules/data/'
 params.pipelines_testdata_base_path = 'https://raw.githubusercontent.com/nf-core/test-datasets/refs/heads/{{ short_name }}'
 
-process {
-    resourceLimits = [
-        cpus: 4,
-        memory: '15.GB',
-        time: '1.h'
-    ]
-}
-
 aws.client.anonymous = true // fixes S3 access issues on self-hosted runners

nf_core/pipelines/lint/nf_test_content.py

@@ -3,7 +3,7 @@
 from pathlib import Path
 from typing import Dict, List, Union
 
-from nf_core.utils import load_tools_config, run_cmd
+from nf_core.utils import load_tools_config
 
 log = logging.getLogger(__name__)
 
@@ -124,26 +124,6 @@ def nf_test_content(self) -> Dict[str, List[str]]:
     # Content of nextflow.config file
     conf_fn = Path(self.wf_path, "tests", "nextflow.config")
 
-    # Get the CPU, memory and time values defined in the test profile configuration.
-    cmd = f"config -profile test -flat {self.wf_path}"
-    result = run_cmd("nextflow", cmd)
-    config_values = {"cpus": "4", "memory": "15.GB", "time": "1.h"}
-    if result is not None:
-        stdout, _ = result
-        for config_line in stdout.splitlines():
-            ul = config_line.decode("utf-8")
-            try:
-                k, v = ul.split(" = ", 1)
-                if k == "cpus":
-                    config_values["cpus"] = v.strip("'\"")
-                elif k == "memory":
-                    config_values["memory"] = v.strip("'\"")
-                elif k == "time":
-                    config_values["time"] = v.strip("'\"")
-            except ValueError:
-                log.debug(f"Couldn't find key=value config pair:\n  {ul}")
-                pass
-
     config_checks: Dict[str, Dict[str, str]] = {
         "modules_testdata_base_path": {
             "pattern": "modules_testdata_base_path",
@@ -153,18 +133,6 @@ def nf_test_content(self) -> Dict[str, List[str]]:
             "pattern": "pipelines_testdata_base_path",
             "description": "`pipelines_testdata_base_path`",
         },
-        "cpus": {
-            "pattern": f"cpus: *[\"']?{config_values['cpus']}[\"']?",
-            "description": f"correct CPU resource limits. Should be {config_values['cpus']}",
-        },
-        "memory": {
-            "pattern": f"memory: *[\"']?{config_values['memory']}[\"']?",
-            "description": f"correct memory resource limits. Should be {config_values['memory']}",
-        },
-        "time": {
-            "pattern": f"time: *[\"']?{config_values['time']}[\"']?",
-            "description": f"correct time resource limits. Should be {config_values['time']}",
-        },
     }
 
     if nf_test_content_conf is None or str(conf_fn.relative_to(self.wf_path)) not in nf_test_content_conf:

tests/pipelines/lint/test_nf_test_content.py

@@ -28,24 +28,16 @@ def test_nf_test_content_nf_test_files(self):
         assert "'tests/test.nf.test' does not snapshot a 'versions.yml' file" in result["failed"]
 
     def test_nf_test_content_nextflow_config_file(self):
-        """Test failure if nextflow.config does not contain correct resource limits."""
-        # Create nextflow.config without resource limits or required parameters
+        """Test failure if nextflow.config does not contain correct parameters."""
+        # Create nextflow.config without required parameters
         config_file = Path(self.new_pipeline) / "tests" / "nextflow.config"
         with open(config_file, "w") as f:
-            f.write("// Missing resource limits and parameters")
+            f.write("// Missing parameters")
         lint_obj = nf_core.pipelines.lint.PipelineLint(self.new_pipeline)
         result = lint_obj.nf_test_content()
         assert len(result["failed"]) > 0
         assert "'tests/nextflow.config' does not contain `modules_testdata_base_path`" in result["failed"]
         assert "'tests/nextflow.config' does not contain `pipelines_testdata_base_path`" in result["failed"]
-        assert "'tests/nextflow.config' does not contain correct CPU resource limits. Should be 4" in result["failed"]
-        assert (
-            "'tests/nextflow.config' does not contain correct memory resource limits. Should be 15.GB"
-            in result["failed"]
-        )
-        assert (
-            "'tests/nextflow.config' does not contain correct time resource limits. Should be 1.h" in result["failed"]
-        )
 
     def test_nf_test_content_missing_nf_test_config_file(self):
         """Test failure if nf-test.config does not contain required settings."""