From aef401d49e495c4bd920865c111bb2456384e9e1 Mon Sep 17 00:00:00 2001 From: rhpvorderman <r.h.p.vorderman@lumc.nl> Date: Thu, 11 May 2017 15:42:42 +0200 Subject: [PATCH] Add fix to increase default fastqc memory to 4 GB per core, to make single-threaded runs easier. --- .../src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala | 2 ++ 1 file changed, 2 insertions(+) diff --git a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala index bd20abc40..a2362a8a6 100644 --- a/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala +++ b/biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala @@ -51,6 +51,8 @@ class Fastqc(val parent: Configurable) extends BiopetCommandLineFunction with Ve def versionCommand = executable + " --version" override def defaultThreads = 4 + override def defaultCoreMemory: Double = 4.0 + /** Sets contaminants and adapters when not yet set */ override def beforeGraph() { this.jobOutputFile = new File(output.getParentFile, s".${fastqfile.getName}.fastqc.out") -- GitLab