Commit 1865f3b0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Added default vmem and add log.file as output file

parent d125c2f3
...@@ -24,6 +24,9 @@ class IGVToolsCount(val root: Configurable) extends IGVTools { ...@@ -24,6 +24,9 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
@Output @Output
var wig: Option[File] = None var wig: Option[File] = None
@Output
def logFile = new File(jobLocalDir, "igv.log")
var maxZoom: Option[Int] = config("maxZoom") var maxZoom: Option[Int] = config("maxZoom")
var windowSize: Option[Int] = config("windowSize") var windowSize: Option[Int] = config("windowSize")
var extFactor: Option[Int] = config("extFactor") var extFactor: Option[Int] = config("extFactor")
...@@ -41,9 +44,17 @@ class IGVToolsCount(val root: Configurable) extends IGVTools { ...@@ -41,9 +44,17 @@ class IGVToolsCount(val root: Configurable) extends IGVTools {
var pairs: Boolean = config("pairs", default = false) var pairs: Boolean = config("pairs", default = false)
override val defaultVmem = "4G"
override def beforeGraph { override def beforeGraph {
super.beforeGraph super.beforeGraph
(tdf, wig) match {
case (Some(tdf), _) => jobLocalDir = tdf.getParentFile
case (_, Some(wig)) => jobLocalDir = wig.getParentFile
case _ => throw new IllegalArgumentException("Must have a wig or tdf file")
}
wig.foreach(x => if (!x.getAbsolutePath.endsWith(".wig")) wig.foreach(x => if (!x.getAbsolutePath.endsWith(".wig"))
throw new IllegalArgumentException("WIG file should have a .wig file-extension")) throw new IllegalArgumentException("WIG file should have a .wig file-extension"))
tdf.foreach(x => if (!x.getAbsolutePath.endsWith(".tdf")) tdf.foreach(x => if (!x.getAbsolutePath.endsWith(".tdf"))
......
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