Merge pull request #1047 from U-BDS/master

Cheaha strict syntax conversion

Author: jfy133

conf/cheaha.config

@@ -1,5 +1,12 @@
+// Prevent schemas warnings for profile parameters
+validation {
+    ignoreParams = [
+        'cheaha_scratch_dir'
+    ]
+}
+
 // Define the Scratch directory
-def scratch_dir = System.getenv("USER_SCRATCH") ?: "/tmp"
+params.cheaha_scratch_dir = env('USER_SCRATCH') ?: '/tmp'
 
 params {
     config_profile_name = 'cheaha'
@@ -9,40 +16,14 @@ params {
 }
 
 env {
-    TMPDIR="$scratch_dir"
-    SINGULARITY_TMPDIR="$scratch_dir"
+    TMPDIR=params.cheaha_scratch_dir
+    SINGULARITY_TMPDIR=params.cheaha_scratch_dir
 }
 
 singularity {
     enabled = true
     autoMounts = true
-    runOptions = "--contain --workdir $scratch_dir -B /scratch"
-}
-
-def getQueues = { time, memory ->
-    def queue_list = ["long"]
-
-    if (time <= 2.h) {
-        queue_list.add("express")
-    }
-
-    if (time <= 12.h) {
-        queue_list.add("short")
-    }
-
-    if (time <= 50.h) {
-        queue_list.add("medium")
-    }
-
-    if (memory >= 300.GB) {
-        queue_list.add("largemem-long")
-
-        if (time <= 50.h) {
-            queue_list.add("largemem")
-        }
-    }
-
-    return queue_list.join(",")
+    runOptions = "--contain --workdir ${params.cheaha_scratch_dir} -B /scratch"
 }
 
 process {
@@ -54,5 +35,29 @@ process {
     executor = 'slurm'
     maxRetries = 3
     beforeScript = 'module load Singularity/3.5.2-GCC-5.4.0-2.26'
-    queue = { getQueues( task.time, task.memory ) }
-}
+    queue = { 
+        def queue_list = ["long"]
+        
+        if (task.time <= 2.h) {
+            queue_list.add("express")
+        }
+
+        if (task.time <= 12.h) {
+            queue_list.add("short")
+        }
+
+        if (task.time <= 50.h) {
+            queue_list.add("medium")
+        }
+
+        if (task.memory >= 300.GB) {
+            queue_list.add("largemem-long")
+
+            if (task.time <= 50.h) {
+                queue_list.add("largemem")
+            }
+        }
+
+        return queue_list.join(",")        
+    }
+}