fix(assembler): do not skip flavor (#350)

* fix(assembler): do not skip flavor * fix(assembly): do not use xlarge
metagenomics · Feb 22, 2024 · 8ec47be · 8ec47be
1 parent efd1725
commit 8ec47be
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Showing 2 changed files with 37 additions and 7 deletions.
diff --git a/main.nf b/main.nf
@@ -5,7 +5,7 @@ include { wSaveSettingsList } from './modules/config/module'
 include { pPublish as pPublishIllumina; pPublish as pPublishOnt; } from './modules/utils/processes'
 include { wShortReadQualityControlFile; wShortReadQualityControlList} from './modules/qualityControl/shortReadQC'
 include { wOntQualityControlFile; wOntQualityControlList} from './modules/qualityControl/ontQC'
-include { wShortReadAssemblyFile; wShortReadAssemblyList } from './modules/assembly/shortReadAssembler'
+include { wShortReadAssemblyFile; wShortReadAssemblyList; wTestMemSelection } from './modules/assembly/shortReadAssembler'
 include { wOntAssemblyFile; wOntAssemblyList } from './modules/assembly/ontAssembler'
 include { wShortReadBinningList } from './modules/binning/shortReadBinning'
 include { wLongReadBinningList } from './modules/binning/ontBinning'

diff --git a/modules/assembly/shortReadAssembler.nf b/modules/assembly/shortReadAssembler.nf
@@ -78,7 +78,7 @@ def getNextHigherResource = { exitCodes, exitStatus, resourceType, attempt, memo
                          return currentResourceType;
                       } else {
                          // if the exit code is not known then the memory value should not be increased
-                         FLAVOR_INDEX_CONSTANT_TO_ADD = 0
+                         FLAVOR_INDEX_CONSTANT_TO_ADD = 1
                          def currentResource = getResources(memory, tool, defaults, sample, FLAVOR_INDEX_CONSTANT_TO_ADD);
                          def currentResourceType = currentResource[resourceType];
 
@@ -148,6 +148,30 @@ process pMetaspades {
 }
 
 
+/*
+*
+* This workflow is only meant for testing purposes.
+*
+*/
+workflow wTestMemSelection {
+  main:
+        exitCode = -9
+        attempt = 2
+        flavorRAMPredicted = "34"
+        resourcesFlavor =  params.resources.highmemXLarge
+        outCPUs = getNextHigherResource([-9, 137, 247], exitCode, "cpus", attempt, \
+        flavorRAMPredicted, params.steps.assembly.megahit, \
+        resourcesFlavor, "SAMPLE")
+
+        outRAM = getNextHigherResource([-9, 137, 247], exitCode, "memory", attempt, \
+        flavorRAMPredicted, params.steps.assembly.megahit, \
+        resourcesFlavor, "SAMPLE")
+
+        println("CPUs: " + outCPUs)
+        println("RAM: " + outRAM)
+}
+
+
 
 /*
  * Input: 
@@ -255,6 +279,8 @@ def getResources(predictedMemory, assembler, defaults, sample, attempt){
      // get memory values as list
      def memorySet = memoryLabelMap.keySet().sort()
 
+
+
      switch(assembler.resources.RAM.mode){
        case 'PREDICT':
      	  def predictedMemoryCeil = (int)Math.ceil(Float.parseFloat(predictedMemory))
@@ -264,7 +290,7 @@ def getResources(predictedMemory, assembler, defaults, sample, attempt){
      	  def sortedUpdatedMemorySet = updatedMemorySet.sort()
      	  def predictedMemoryIndex = sortedUpdatedMemorySet.findIndexOf({ it == predictedMemoryCeil })
 
-     	  def nextHigherMemoryIndex = predictedMemoryIndex + attempt + 1
+     	  def nextHigherMemoryIndex = predictedMemoryIndex + attempt
 
      	  if(nextHigherMemoryIndex  >= sortedUpdatedMemorySet.size()){
              // In case it is already the highest possible memory setting
@@ -293,19 +319,23 @@ def getResources(predictedMemory, assembler, defaults, sample, attempt){
        	  }
           break;
        case 'DEFAULT':
+
           // If the memory value is not predicted do the following
           def defaultCpus = defaults.cpus
+
           def defaultMemory = defaults.memory
 
      	  def defaultMemoryIndex = memorySet.findIndexOf({ it == defaultMemory })
 
- 	  def nextHigherMemoryIndex = defaultMemoryIndex + attempt
+ 	  def nextHigherMemoryIndex = defaultMemoryIndex + attempt - 1 
 
-     	  if(defaultMemoryIndex >= memorySet.size()){
+
+     	  if(nextHigherMemoryIndex >= memorySet.size()){
              // In case it is already the highest possible memory setting
              // then try the label with the highest memory
-             println("Warning: Predicted Memory " + predictedMemoryCeil \
-		+ " of the dataset " + sample + " is greater or equal to the flavour with the largest RAM specification.")
+             println("Warning: Highest possible memory setting " \
+		+ " of the dataset " + sample + " is already reached." \
+                + " Retry will be done using a flavor with the highest possible RAM configuration")
 
              def label = memoryLabelMap[memorySet[memorySet.size()-1]]
              def cpus =  labelMap[label]["cpus"]