Fix nextflow.config

Commands now run using the shell

Author: Alan Christie

src/jote/compose.py

@@ -36,10 +36,8 @@
 """
 
 _NF_CONFIG_CONTENT: str = """
-docker {
-  enabled = true
-  runOptions = '-u $(id -u):$(id -g)'
-}
+docker.enabled = true
+docker.runOptions = '-u $(id -u):$(id -g)'
 """
 
 

src/jote/jote.py

@@ -329,10 +329,11 @@ def _run_nextflow(command: str,
     os.chdir(project_path)
 
     try:
-        test = subprocess.run(command.split(),
+        test = subprocess.run(command,
+                              shell=True,
+                              check=False,
                               capture_output=True,
-                              timeout=timeout_minutes * 60,
-                              check=False)
+                              timeout=timeout_minutes * 60)
     finally:
         os.chdir(cwd)