added memory option

cwl/pilon/pilon.cwl

@@ -26,6 +26,11 @@ inputs:
     inputBinding:
       prefix: --threads
     default: 2
+  memory:
+    type: int?
+    doc: maximum memory usage in megabytes
+    label: memory usage (mb)
+    default: 8000
 
   assembly:
     type: File
@@ -40,8 +45,8 @@ inputs:
     doc: Indexed sorted bam file with mapped reads to draft assembly
     inputBinding:
       prefix: --frags
-    secondaryFiles:
-      - .bai
+    # secondaryFiles:
+    #   - .bai
   fixlist:
     type: string?
     label: Fix List
@@ -63,10 +68,12 @@ inputs:
     inputBinding:
       prefix: --vcf
 
-
-baseCommand: ["java", "-jar","/unlock/infrastructure/binaries/Pilon/pilon-1.24.jar"]
+baseCommand: ["java"]
 
 arguments:
+  - "-jar"
+  - "-Xmx$(inputs.memory)M"
+  - "/unlock/infrastructure/binaries/Pilon/pilon-1.24.jar"
   - valueFrom: $(inputs.identifier)_scaffolds_polished
     prefix: "--output"