Commit ffc8be9b authored by sajvanderzeeuw's avatar sajvanderzeeuw
Browse files

GC options can now be set through the config

parent 6b7aaacf
...@@ -5,6 +5,10 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction ...@@ -5,6 +5,10 @@ import org.broadinstitute.gatk.queue.function.JavaCommandLineFunction
trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait { trait BiopetJavaCommandLineFunction extends JavaCommandLineFunction with BiopetCommandLineFunctionTrait {
executable = "java" executable = "java"
javaGCThreads = config("java_gc_threads")
javaGCHeapFreeLimit = config("java_gc_heap_freelimit")
javaGCTimeLimit = config("java_gc_timelimit")
override def afterGraph { override def afterGraph {
memoryLimit = config("memory_limit") memoryLimit = config("memory_limit")
} }
......
...@@ -6,7 +6,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument } ...@@ -6,7 +6,6 @@ import org.broadinstitute.gatk.utils.commandline.{ Input, Output, Argument }
class SamToFastq(val root: Configurable) extends Picard { class SamToFastq(val root: Configurable) extends Picard {
javaMainClass = "picard.sam.SamToFastq" javaMainClass = "picard.sam.SamToFastq"
javaGCThreads = config("gcthreads", default = 2)
@Input(doc = "The input SAM or BAM files to analyze.", required = true) @Input(doc = "The input SAM or BAM files to analyze.", required = true)
var input: File = _ var input: File = _
......
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