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biopet.biopet
Commits
206c7f01
Commit
206c7f01
authored
Sep 25, 2015
by
Peter van 't Hof
Browse files
Fix fastqc dependency
parent
7a3bf3b2
Changes
1
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Inline
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public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
206c7f01
...
...
@@ -3,7 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import
java.io.File
import
nl.lumc.sasc.biopet.core.
{
BiopetCommandLineFunction
,
BiopetPipe
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Gzip
,
Sickle
,
Cutadapt
}
import
nl.lumc.sasc.biopet.extensions.seqtk.SeqtkSeq
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.utils.commandline.
{
Output
,
Input
}
...
...
@@ -31,7 +31,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
override
def
beforeGraph
()
:
Unit
=
{
super
.
beforeGraph
()
require
(
read
!=
null
)
deps
::
:
=
fastqc
.
output
Files
deps
::=
output
}
override
def
defaultCoreMemory
=
2.0
...
...
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