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biopet.biopet
Commits
fe542841
Commit
fe542841
authored
Dec 03, 2015
by
Peter van 't Hof
Browse files
Style fixes
parent
7cca44be
Changes
2
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protected/biopet-gatk-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/gatk/broad/UnifiedGenotyper.scala
View file @
fe542841
...
...
@@ -15,7 +15,6 @@ class UnifiedGenotyper(val root: Configurable) extends org.broadinstitute.gatk.q
@Output
(
required
=
false
)
protected
var
vcfIndex
:
File
=
_
if
(
config
.
contains
(
"scattercount"
))
scatterCount
=
config
(
"scattercount"
)
if
(
config
.
contains
(
"dbsnp"
))
this
.
dbsnp
=
config
(
"dbsnp"
)
sample_ploidy
=
config
(
"ploidy"
)
...
...
public/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/QcCommand.scala
View file @
fe542841
...
...
@@ -133,7 +133,7 @@ class QcCommand(val root: Configurable, val fastqc: Fastqc) extends BiopetComman
outputCommand
match
{
case
gzip
:
Gzip
=>
outputFile
:<:
gzip
case
cat
:
Cat
=>
cat
.
input
=
outputFile
::
Nil
case
cat
:
Cat
=>
cat
.
input
=
outputFile
::
Nil
}
seqtk
.
beforeGraph
()
...
...
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