adjust memory

biopet.wdl

@@ -65,7 +65,7 @@ task SampleConfig {
         set -e -o pipefail
         ${preCommand}
         mkdir -p . ${"$(dirname " + jsonOutputPath + ")"} ${"$(dirname " + tsvOutputPath + ")"}
-        java -Xmx${true=""+memory false="4" defined(memory)}G -jar ${tool_jar} \
+        java -Xmx${true=memory false="4" defined(memory)}G -jar ${tool_jar} \
         -i ${sep="-i " inputFiles} \
         ${"--sample " + sample} \
         ${"--library " + library} \
@@ -101,7 +101,7 @@ task BaseCounter {
         set -e -o pipefail
         ${preCommand}
         mkdir -p ${outputDir}
-        java -Xmx${true=""+memory false="12" defined(memory)}G -jar ${tool_jar} \
+        java -Xmx${true=memory false="12" defined(memory)}G -jar ${tool_jar} \
         -b ${bam} \
         -r ${refFlat} \
         -o ${outputDir} \

fastqc.wdl

@@ -70,7 +70,7 @@ task extractAdapters {
     command {
     set -e
     mkdir -p ${outputDir}
-    java -Xmx${true=""+memory false="4" defined(memory)}G -jar ${extractAdaptersFastqcJar} \
+    java -Xmx${true=memory false="4" defined(memory)}G -jar ${extractAdaptersFastqcJar} \
     --inputFile ${inputFile} \
     ${"--adapterOutputFile " + adapterOutputFilePath } \
     ${"--contamsOutputFile " + contamsOutputFilePath } \
@@ -89,7 +89,7 @@ task extractAdapters {
     }
 
     runtime {
-        memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.0]))
+        memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 2.5]))
     }
 }
 

picard.wdl

@@ -90,7 +90,7 @@ task MarkDuplicates {
         ${preCommand}
         mkdir -p $(dirname ${output_bam_path})
         java ${"-Dsamjdk.compression_level=" + compression_level} \
-        -Xmx${true=memory false="4" defined(memory)}G -jar ${picard_jar} \
+        -Xmx${true=memory false="8" defined(memory)}G -jar ${picard_jar} \
           MarkDuplicates \
           INPUT=${sep=' INPUT=' input_bams} \
           OUTPUT=${output_bam_path} \
@@ -110,7 +110,7 @@ task MarkDuplicates {
     }
 
     runtime {
-        memory: ceil(select_first([memory, 4.0]) * select_first([memoryMultiplier, 1.5]))
+        memory: ceil(select_first([memory, 8.0]) * select_first([memoryMultiplier, 1.5]))
     }
 }