From c0064f43dd4294c372fa3afc612661962c98fec7 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 16:39:13 +0100
Subject: [PATCH] Update Cufflinks defaults for cluster run
---
.../scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
index d3d28f7c1..cc9b0490c 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Cufflinks.scala
@@ -29,6 +29,12 @@ class Cufflinks(val root: Configurable) extends BiopetCommandLineFunction {
/** default executable */
executable = config("exe", default = "cufflinks")
+ /** default threads */
+ override def defaultThreads = num_threads.getOrElse(1)
+
+ /** default vmem for cluster jobs */
+ override def defaultVmem = "4G"
+
/** input file */
@Input(doc = "Input file (SAM or BAM)", required = true)
var input: File = null
--
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