runtime adjustments bwa, exractAdapters

bwa.wdl

@@ -22,7 +22,7 @@ task BwaMem {
         File bamFile = outputPath
     }
     runtime{
-        threads: select_first([threads])
+        threads: if defined(threads) then threads else 1
         memory: if defined(memory) then memory else 8
     }
 }

fastqc.wdl

@@ -65,7 +65,7 @@ task extractAdapters {
     command {
     set -e
     mkdir -p ${outputDir}
-    java -Xmx3G -jar ${extractAdaptersFastqcJar} \
+    java -Xmx4G -jar ${extractAdaptersFastqcJar} \
     --inputFile ${inputFile} \
     ${"--adapterOutputFile " + adapterOutputFilePath } \
     ${"--contamsOutputFile " + contamsOutputFilePath } \