Commit a98db543 authored by bow's avatar bow

Merge branch 'fix-memory' into 'develop'

Raise memory

Fixes #356 

- [x] Check Flexiprep
- [x] Check Toucan
- [x] Check Shiva
- [x] Check Mapping
- [x] Check Gears

See merge request !421
parents 3a5c0f08 2fe05eec
......@@ -58,6 +58,8 @@ class CatVariants(val root: Configurable) extends BiopetJavaCommandLineFunction
@Gather(classOf[org.broadinstitute.gatk.queue.function.scattergather.SimpleTextGatherFunction])
var log_to_file: File = _
override def defaultCoreMemory = 4.0
override def beforeGraph() = {
super.beforeGraph()
if (reference == null) reference = referenceFasta()
......
......@@ -36,7 +36,7 @@ class SeqStat(val root: Configurable) extends ToolCommandFunction with Summariza
@Output(doc = "Output JSON", shortName = "output", required = true)
var output: File = null
override def defaultCoreMemory = 2.5
override def defaultCoreMemory = 4.0
override def cmdLine = super.cmdLine + required("-i", input) + required("-o", output)
......
......@@ -29,6 +29,8 @@ class ValidateFastq(val root: Configurable) extends ToolCommandFunction {
@Input(doc = "Input R1 fastq file", required = false)
var r2Fastq: Option[File] = None
override def defaultCoreMemory = 4.0
override def cmdLine = super.cmdLine +
required("-i", r1Fastq) +
optional("-j", r2Fastq)
......
......@@ -43,7 +43,7 @@ class VcfWithVcf(val root: Configurable) extends ToolCommandFunction with Refere
var fields: List[(String, String, Option[String])] = List()
override def defaultCoreMemory = 2.0
override def defaultCoreMemory = 4.0
override def beforeGraph() {
super.beforeGraph()
......
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