also wrap-up 1st attempt in check_max function to avoid requesting mo…

…re than what is allowed

conf/base.config

@@ -35,8 +35,8 @@ process {
     // Assemblies will first try to adjust themselves to a parallel execution
     // If it is not possible, then it waits to use all the resources allowed
     withLabel:process_assembly {
-      cpus   = {  if (task.attempt == 1) { params.start_asm_cpus } else { params.max_cpus   } }
-      memory = {  if (task.attempt == 1) { params.start_asm_mem  } else { params.max_memory } }
+      cpus   = {  if (task.attempt == 1) { check_max( params.start_asm_cpus, 'cpus'   ) } else { params.max_cpus   } }
+      memory = {  if (task.attempt == 1) { check_max( params.start_asm_mem , 'memory' ) } else { params.max_memory } }
 
       // retry at least once to try it with full resources
       errorStrategy = { task.exitStatus in [1,21,143,137,104,134,139,247] ? 'retry' : 'finish' }
@@ -48,9 +48,9 @@ process {
     def quast_mem  = ((params.start_asm_mem  / 2) > 6.GB) ? (params.start_asm_mem / 2) : 6.GB
     def quast_cpus = ((params.start_asm_cpus / 2) > 4   ) ? (params.start_asm_mem / 2) : 4
     withName:quast {
-      cpus   = {  if (task.attempt == 1) { quast_cpus } else { params.max_cpus   } }
-      memory = {  if (task.attempt == 1) { quast_mem  } else { params.max_memory } }
-      time   = {  if (task.attempt == 1) { check_max( 12.h * task.attempt, 'time' ) } else { params.max_time } }
+      cpus   = {  if (task.attempt == 1) { check_max( params.quast_cpus, 'cpus'   ) } else { params.max_cpus   } }
+      memory = {  if (task.attempt == 1) { check_max( params.quast_mem , 'memory' ) } else { params.max_memory } }
+      time   = {  if (task.attempt == 1) { check_max( 12.h * task.attempt, 'time' ) } else { params.max_time   } }
 
       // retry at least once to try it with full resources
       errorStrategy = { task.exitStatus in [21,143,137,104,134,139,247] ? 'retry' : 'finish' }