initial pass for strict syntax

Author: lianov

conf/cheaha.config

@@ -1,5 +1,13 @@
+// Prevent schemas warnings for profile parameters
+validation {
+    ignoreParams = [
+        'cheaha_scratch_dir',
+        'cheaha_getQueues'
+    ]
+}
+
 // 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'
@@ -9,17 +17,17 @@ 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"
+    runOptions = "--contain --workdir ${params.cheaha_scratch_dir} -B /scratch"
 }
 
-def getQueues = { time, memory ->
+params.cheaha_getQueues = { time, memory ->
     def queue_list = ["long"]
 
     if (time <= 2.h) {
@@ -44,6 +52,7 @@ def getQueues = { time, memory ->
 
     return queue_list.join(",")
 }
+//Note .call() above did not resolve current warning for Nextflow plugin (for queue process below).
 
 process {
     resourceLimits = [
@@ -54,5 +63,5 @@ 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 = { params.cheaha_getQueues( task.time, task.memory ) }
 }