reoptimize for parallel cluster

nextflow.config

@@ -228,10 +228,26 @@ def check_max(obj, type) {
 // --------------------------------------
 
 process{
+  // Default minimal resources
   cpus = { check_max( 1 * task.attempt, 'cpus' ) }
   memory = { check_max( 6.GB * task.attempt, 'memory' ) }
   time = { check_max( 4.h * task.attempt, 'time' ) }
 
+  // Multi core, run 2 simultaneously
+  withName:snippy_pairwise{
+    cpus = Math.max(1, Math.floor(params.max_cpus / 2 ))
+    maxForks = Math.min(2, params.max_cpus)
+  }
+  // Multi core, run 2 simultaneously
+  withName:iqtree{
+    cpus = params.max_cpus
+    maxForks = 1
+  }
+  withName:eager{
+    cpus = params.max_cpus
+    maxForks = 1
+  }
+
   errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' }
   maxRetries = 3
   maxErrors = '-1'
@@ -243,7 +259,5 @@ process{
 
 executor{
   name = 'local'
-  queueSize = 2
-  cpus = 2
-  memory = '6 GB'
+  queueSize = params.max_cpus
 }