nf-core · maxulysse · Oct 7, 2019 · Oct 7, 2019 · Oct 7, 2019 · Oct 7, 2019
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -17,6 +17,7 @@
 * New Slack channel badge in pipeline readme
 * Add AWS CI tests and full tests GitHub Actions workflows
 * Update AWS CI tests and full tests secrets names
+* Replace and improve `check_max()` with `set_resource()`, which is already used in `nf-core/sarek`
 
 ### Linting
 

diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/base.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/base.config
@@ -3,7 +3,7 @@
  *  {{ cookiecutter.name }} Nextflow base config file
  * -------------------------------------------------
  * A 'blank slate' config file, appropriate for general
- * use on most high performace compute environments.
+ * use on most high performance compute environments.
  * Assumes that all software is installed and available
  * on the PATH. Runs in `local` mode - all jobs will be
  * run on the logged in environment.
@@ -12,9 +12,9 @@
 process {
 
   // TODO nf-core: Check the defaults for all processes
-  cpus = { check_max( 1 * task.attempt, 'cpus' ) }
-  memory = { check_max( 7.GB * task.attempt, 'memory' ) }
-  time = { check_max( 4.h * task.attempt, 'time' ) }
+  cpus = { set_resource(1 * task.attempt) }
+  memory = { set_resource(7.GB * task.attempt) }
+  time = { set_resource(4.h * task.attempt) }
 
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 1
@@ -27,25 +27,25 @@ process {
   // TODO nf-core: Customise requirements for specific processes.
   // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors
   withLabel:process_low {
-    cpus = { check_max( 2 * task.attempt, 'cpus' ) }
-    memory = { check_max( 14.GB * task.attempt, 'memory' ) }
-    time = { check_max( 6.h * task.attempt, 'time' ) }
+    cpus = { set_resource(2 * task.attempt) }
+    memory = { set_resource(14.GB * task.attempt) }
+    time = { set_resource(6.h * task.attempt) }
   }
   withLabel:process_medium {
-    cpus = { check_max( 6 * task.attempt, 'cpus' ) }
-    memory = { check_max( 42.GB * task.attempt, 'memory' ) }
-    time = { check_max( 8.h * task.attempt, 'time' ) }
+    cpus = { set_resource(6 * task.attempt) }
+    memory = { set_resource(42.GB * task.attempt) }
+    time = { set_resource(8.h * task.attempt) }
   }
   withLabel:process_high {
-    cpus = { check_max( 12 * task.attempt, 'cpus' ) }
-    memory = { check_max( 84.GB * task.attempt, 'memory' ) }
-    time = { check_max( 10.h * task.attempt, 'time' ) }
+    cpus = { set_resource(12 * task.attempt) }
+    memory = { set_resource(84.GB * task.attempt) }
+    time = { set_resource(10.h * task.attempt) }
   }
   withLabel:process_long {
-    time = { check_max( 20.h * task.attempt, 'time' ) }
+    time = { set_resource(20.h * task.attempt) }
   }
   withName:get_software_versions {
     cache = false
   }
-  
+
 }
diff --git a/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config b/nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
@@ -116,35 +116,18 @@ manifest {
   version = '{{ cookiecutter.version }}'
 }
 
-// Function to ensure that resource requirements don't go beyond
-// a maximum limit
-def check_max(obj, type) {
-  if (type == 'memory') {
-    try {
-      if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
-        return params.max_memory as nextflow.util.MemoryUnit
-      else
-        return obj
-    } catch (all) {
-      println "   ### ERROR ###   Max memory '${params.max_memory}' is not valid! Using default value: $obj"
+// Set compute resources to minimum between requested value and the corresponding value in params max_cpus, max_memory or max_time
+def set_resource(obj) {
+  try {
+    if (obj.getClass() == nextflow.util.MemoryUnit && obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1)
+      return params.max_memory as nextflow.util.MemoryUnit
+    else if (obj.getClass() == nextflow.util.Duration && obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
+      return params.max_time as nextflow.util.Duration
+    else if (obj.getClass() == java.lang.Integer)
+      return Math.min(obj, params.max_cpus as int)
+    else
       return obj
-    }
-  } else if (type == 'time') {
-    try {
-      if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1)
-        return params.max_time as nextflow.util.Duration
-      else
-        return obj
-    } catch (all) {
-      println "   ### ERROR ###   Max time '${params.max_time}' is not valid! Using default value: $obj"
-      return obj
-    }
-  } else if (type == 'cpus') {
-    try {
-      return Math.min( obj, params.max_cpus as int )
-    } catch (all) {
-      println "   ### ERROR ###   Max cpus '${params.max_cpus}' is not valid! Using default value: $obj"
-      return obj
-    }
+  } catch (all) {
+      println "   ### ERROR ###   Max params max_memory:'${params.max_memory}', max_time:'${params.max_time}' or max_cpus:'${params.max_cpus}'  is not valid! Using default value: $obj"
   }
 }