Commit a508e6f8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

changed default memory

parent 31b7ebfc
...@@ -311,6 +311,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with ...@@ -311,6 +311,8 @@ trait CommandLineGATK extends BiopetJavaCommandLineFunction with Reference with
override def versionExitcode = List(0, 1) override def versionExitcode = List(0, 1)
def versionCommand = executable + " -jar " + jarFile + " -version" def versionCommand = executable + " -jar " + jarFile + " -version"
override def defaultCoreMemory = 4.0
override def faiRequired = true
override def dictRequired = true override def dictRequired = true
override def beforeGraph() { override def beforeGraph() {
......
...@@ -397,8 +397,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt ...@@ -397,8 +397,6 @@ class HaplotypeCaller(val root: Configurable) extends CommandLineGATK with Scatt
@Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "") @Argument(fullName = "filter_bases_not_stored", shortName = "filterNoBases", doc = "Filter out reads with no stored bases (i.e. '*' where the sequence should be), instead of failing with an error", required = false, exclusiveOf = "", validation = "")
var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false) var filter_bases_not_stored: Boolean = config("filter_bases_not_stored", default = false)
override def defaultCoreMemory = 3.0
override def beforeGraph() { override def beforeGraph() {
super.beforeGraph() super.beforeGraph()
if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out)) if (out != null && !org.broadinstitute.gatk.utils.io.IOUtils.isSpecialFile(out))
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