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biopet.biopet
Commits
aef401d4
Commit
aef401d4
authored
May 11, 2017
by
Ruben Vorderman
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Add fix to increase default fastqc memory to 4 GB per core, to make single-threaded runs easier.
parent
0cef5b4b
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
...rc/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
+2
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biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/Fastqc.scala
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aef401d4
...
...
@@ -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"
)
...
...
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