use nextflow config to obtain resource limit values

Author: mirpedrol

nf_core/pipelines/lint/nf_test_content.py

@@ -1,8 +1,11 @@
+import logging
 import re
 from pathlib import Path
 from typing import Dict, List, Union
 
-from nf_core.utils import load_tools_config
+from nf_core.utils import load_tools_config, run_cmd
+
+log = logging.getLogger(__name__)
 
 
 def nf_test_content(self) -> Dict[str, List[str]]:
@@ -120,6 +123,27 @@ 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",
@@ -130,16 +154,16 @@ def nf_test_content(self) -> Dict[str, List[str]]:
             "description": "`pipelines_testdata_base_path`",
         },
         "cpus": {
-            "pattern": "cpus: *[\"']?4[\"']?",
-            "description": "correct CPU resource limits. Should be 4",
+            "pattern": f"cpus: *[\"']?{config_values['cpus']}[\"']?",
+            "description": f"correct CPU resource limits. Should be {config_values['cpus']}",
         },
         "memory": {
-            "pattern": "memory: *[\"']?15\.GB[\"']?",
-            "description": "correct memory resource limits. Should be 15.GB",
+            "pattern": f"memory: *[\"']?{config_values['memory']}[\"']?",
+            "description": f"correct memory resource limits. Should be {config_values['memory']}",
         },
         "time": {
-            "pattern": "time: *[\"']?1\.h[\"']?",
-            "description": "correct time resource limits. Should be 1.h",
+            "pattern": f"time: *[\"']?{config_values['time']}[\"']?",
+            "description": f"correct time resource limits. Should be {config_values['time']}",
         },
     }