From 3ed93bee386a02693eb077e7bd0e98f1ed54fb7b Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Sun, 8 Mar 2015 16:38:17 +0100
Subject: [PATCH] Update GSNAP defaults for cluster run
---
.../main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala | 6 ++++++
1 file changed, 6 insertions(+)
diff --git a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
index 826ac058a..a518e7246 100644
--- a/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
+++ b/public/biopet-framework/src/main/scala/nl/lumc/sasc/biopet/extensions/Gsnap.scala
@@ -22,6 +22,12 @@ class Gsnap(val root: Configurable) extends BiopetCommandLineFunction {
/** default executable */
executable = config("exe", default = "gsnap", freeVar = false)
+ /** default threads */
+ override def defaultThreads = nthreads.getOrElse(1)
+
+ /** default vmem for cluster jobs */
+ override def defaultVmem = "4G"
+
/** input file */
@Input(doc = "Input FASTQ file(s)", required = true) //var input: List[File] = _
var input: List[File] = List.empty[File]
--
GitLab