Merge pull request #163 from biowdl/BIOWDL-357

update memory for combine gvcfs

CHANGELOG.md

@@ -11,6 +11,10 @@ that users understand how the changes affect the new version.
 
 version 2.1.0-dev
 ---------------------------
++ Make intervals optional for GATK CombineGVCFs
++ Updated biowdl-input-converter version.
++ GATK CombineGVCFs memory was tripled to prevent it from using a lot of CPU in
+  Garbage Collection mode.
 + Updated parameter_meta sections for Minimap2 and TranscriptClean to wdl-aid format.
 + Updated cores variable for TALON, the default is now 4.
 + Updated TALON to version 4.4.

biowdl.wdl

@@ -31,7 +31,7 @@ task InputConverter {
         Boolean skipFileCheck=true
         Boolean checkFileMd5sums=false
         Boolean old=false
-        String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.0--py_0"
+        String dockerImage = "quay.io/biocontainers/biowdl-input-converter:0.2.1--py_0"
     }
 
     command <<<

gatk.wdl

@@ -95,14 +95,14 @@ task CombineGVCFs {
     input {
         Array[File]+ gvcfFiles
         Array[File]+ gvcfFilesIndex
-        Array[File]+ intervals
+        Array[File] intervals = []
         String outputPath
         File referenceFasta
         File referenceFastaDict
         File referenceFastaFai
 
-        String memory = "12G"
-        String javaXmx = "4G"
+        String memory = "24G"
+        String javaXmx = "12G"
         String dockerImage = "quay.io/biocontainers/gatk4:4.1.0.0--0"
     }
 
@@ -114,7 +114,7 @@ task CombineGVCFs {
         -R ~{referenceFasta} \
         -O ~{outputPath} \
         -V ~{sep=' -V ' gvcfFiles} \
-        -L ~{sep=' -L ' intervals}
+        ~{true='-L' false='' length(intervals) > 0} ~{sep=' -L ' intervals}
     }
 
     output {