More robust parsing of shm-size containerOptions

This commit ensures that the `shm-size` option is correctly parsed from the containerOptions. This is necessary to ensure that the correct value in MiB is passed to the AWS Batch API when creating a job definition.

Signed-off-by: Rob Syme <[email protected]>

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsContainerOptionsMapper.groovy

@@ -22,6 +22,7 @@ import com.amazonaws.services.batch.model.Tmpfs
 import com.amazonaws.services.batch.model.Ulimit
 import groovy.transform.CompileStatic
 import nextflow.util.CmdLineOptionMap
+import nextflow.util.MemoryUnit
 
 /**
  * Maps task container options to AWS container properties
@@ -106,7 +107,8 @@ class AwsContainerOptionsMapper {
         // shared Memory Size
         def value = findOptionWithSingleValue(options, 'shm-size')
         if ( value ) {
-            params.setSharedMemorySize(value as Integer)
+            MemoryUnit sharedMemorySize = (value as MemoryUnit)
+            params.setSharedMemorySize(sharedMemorySize.mega as Integer)
             atLeastOneSet = true
         }
 
@@ -156,6 +158,7 @@ class AwsContainerOptionsMapper {
      * @return the value, if any, or empty
      */
     protected static String findOptionWithSingleValue(CmdLineOptionMap options, String name) {
+        println "Inside findOptionWithSingleValue looking for $name in $options"
         options.getFirstValueOrDefault(name,null) as String
     }