Fixes to runtime attributes for workflows for new GCP Batch engine (#501)

* Fixed all `bootDiskSizeGb` entries to be ints.

Author: jonn-smith

.dockstore.yml

@@ -176,4 +176,4 @@ workflows:
   primaryDescriptorPath: /wdl/pipelines/TechAgnostic/TertiaryAnalysis/ExtractSnpBarcodeFromVcfFile.wdl
 - name: QCAssessmentDepthBased
   subclass: wdl
-  primaryDescriptorPath: /wdl/pipelines/ILMN/QualityControl/QCAssessmentDepthBased.wdl
+  primaryDescriptorPath: /wdl/pipelines/ILMN/QualityControl/QCAssessmentDepthBased.wdl

wdl/deprecated/tasks/dsde_pipelines_tasks/BamProcessing.wdl

@@ -81,7 +81,7 @@ task SortSamSpark {
   runtime {
     docker: gatk_docker
     disks: "local-disk " + disk_size + " HDD"
-    bootDiskSizeGb: "15"
+    bootDiskSizeGb: 15
     cpu: "16"
     memory: "102 GiB"
     preemptible: preemptible_tries
@@ -192,7 +192,7 @@ task MarkDuplicatesSpark {
   runtime {
     docker: "jamesemery/gatknightly:gatkMasterSnapshot44ca2e9e84a"
     disks: "/mnt/tmp " + ceil(2.1 * total_input_size) + " LOCAL, local-disk " + disk_size + " HDD"
-    bootDiskSizeGb: "50"
+    bootDiskSizeGb: 50
     cpu: cpu_size
     memory: "~{memory_size} GiB"
     preemptible: preemptible_tries

wdl/pipelines/TechAgnostic/Utility/BenchmarkVCFs.wdl

@@ -530,7 +530,7 @@ task CheckForVariants {
             docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
             preemptible: select_first([preemptible,0])
             disks: "local-disk " + disk_size + " HDD"
-            bootDiskSizeGb: "16"
+            bootDiskSizeGb: 16
             memory: memoryRam + " GB"
     }
 
@@ -775,7 +775,7 @@ task EvalGATKGC {
         docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
         preemptible: select_first([preemptible,0])
         disks: "local-disk " + disk_size + " HDD"
-        bootDiskSizeGb: "16"
+        bootDiskSizeGb: 16
         memory: memoryRam + " GB"
     }
 
@@ -843,7 +843,7 @@ task ConvertIntervals {
         docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
         preemptible: select_first([preemptible,0])
         disks: "local-disk " + disk_size + " HDD"
-        bootDiskSizeGb: "16"
+        bootDiskSizeGb: 16
         memory: memoryRam + " GB"
     }
 
@@ -882,7 +882,7 @@ task FixVcfHeader {
             docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
             preemptible: select_first([preemptible,0])
             disks: "local-disk " + disk_size + " HDD"
-            bootDiskSizeGb: "16"
+            bootDiskSizeGb: 16
             memory: memoryRam + " GB"
     }
 
@@ -923,7 +923,7 @@ task CountUNKVcfEval {
                 docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
                 preemptible: select_first([preemptible,0])
                 disks: "local-disk " + disk_size + " HDD"
-                bootDiskSizeGb: "16"
+                bootDiskSizeGb: 16
                 memory: memoryRam + " GB"
     }
     output {
@@ -967,7 +967,7 @@ task CountUNKGC {
                     docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
                     preemptible: select_first([preemptible,0])
                     disks: "local-disk " + disk_size + " HDD"
-                    bootDiskSizeGb: "16"
+                    bootDiskSizeGb: 16
                     memory: memoryRam + " GB"
         }
 
@@ -1043,7 +1043,7 @@ task EvalForVariantSelection {
             docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
             preemptible: select_first([preemptible,0])
             disks: "local-disk " + disk_size + " HDD"
-            bootDiskSizeGb: "16"
+            bootDiskSizeGb: 16
             memory: memoryRam + " GB"
     }
 
@@ -1483,7 +1483,7 @@ task MatchEvalTruth {
             docker: "us.gcr.io/broad-gatk/gatk:"+gatkTag
             preemptible: select_first([preemptible,0])
             disks: "local-disk " + disk_size + " HDD"
-            bootDiskSizeGb: "16"
+            bootDiskSizeGb: 16
             memory: memoryRam + " GB"
         }
 }

wdl/pipelines/Z_One_Off_Analyses/BroadOnPremMalariaPipeline_1_Alignment_and_Variant_Calling.wdl

@@ -685,7 +685,7 @@ task Error {
         docker: "ubuntu:22.04"
         memory: "512 MB"
         disks: "local-disk 10 HDD"
-        bootDiskSizeGb: "10"
+        bootDiskSizeGb: 10
         preemptible: 1
         cpu: 1
     }

wdl/tasks/Utility/Utils.wdl

@@ -1746,7 +1746,7 @@ task GetCurrentTimestampString {
          docker: "ubuntu:19.10"
          memory: "512 MB"
          disks: "local-disk 10 HDD"
-         bootDiskSizeGb: "15"
+         bootDiskSizeGb: 15
          preemptible: 0
          cpu: 1
      }