Update sortsam task with extra variables

picard.wdl

@@ -654,9 +654,15 @@ task SortSam {
     input {
         File inputBam
         String outputPath
-
-        Int XmxGb = 4
-        Int memoryGb = 1 + XmxGb
+        Boolean sortByName = false
+        Boolean createIndex = true
+        Boolean createMd5File = false
+        Int maxRecordsInRam = 500000
+        Int compressionLevel = 1
+
+        # Default ram of 4 GB. Using 125001.0  to prevent an answer of 
+        # 4.000000001 which gets rounded to 5.
+        Int XmxGb = ceil(maxRecordsInRam / 125001.0)
         Int timeMinutes = 1 + ceil(size(inputBam, "G") * 2)
         # A mulled container is needed to have both picard and bwa in one container.
         # This container contains: picard (2.18.7), bwa (0.7.17-r1188)
@@ -664,12 +670,17 @@ task SortSam {
     }
 
     command {
+        set -e
         mkdir -p "$(dirname ~{outputPath})"
         picard -Xmx~{XmxGb}G -XX:ParallelGCThreads=1 SortSam \
         INPUT=~{inputBam} \
         OUTPUT=~{outputPath} \
-        SORT_ORDER=coordinate \
-        CREATE_INDEX=true
+        MAX_RECORDS_IN_RAM=~{maxRecordsInRam} \
+        SORT_ORDER=~{true="queryname" false="coordinate" sortByName} \
+        CREATE_INDEX=~{true="true" false="false" createIndex} \
+        COMPRESSION_LEVEL=~{compressionLevel} \
+        CREATE_MD5_FILE=~{true="true" false="false" createMd5File}
+
     }
 
     output {
@@ -679,7 +690,7 @@ task SortSam {
 
     runtime {
         cpu: 1
-        memory: "~{memoryGb}G"
+        memory: "~{1 + XmxGb}G"
         time_minutes: timeMinutes
         docker: dockerImage
     }
@@ -687,7 +698,6 @@ task SortSam {
     parameter_meta {
         inputBam: {description: "The unsorted input BAM file", category: "required"}
         outputPath: {description: "The location the output BAM file should be written to.", category: "required"}
-        memoryGb: {description: "The amount of memory this job will use.", category: "advanced"}
         XmxGb: {description: "The maximum memory available to picard SortSam. Should be lower than `memory` to accommodate JVM overhead and BWA mem's memory usage.",
                   category: "advanced"}
         timeMinutes: {description: "The maximum amount of time the job will run in minutes.", category: "advanced"}