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biopet.biopet
Commits
9c297111
Commit
9c297111
authored
Jul 21, 2017
by
Peter van 't Hof
Browse files
Added shiva report to Basty
parent
d7ef6f44
Changes
1
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Inline
Side-by-side
basty/src/main/scala/nl/lumc/sasc/biopet/pipelines/basty/Basty.scala
View file @
9c297111
...
...
@@ -21,9 +21,10 @@ package nl.lumc.sasc.biopet.pipelines.basty
import
java.io.File
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.
{
MultiSampleQScript
,
PipelineCommand
}
import
nl.lumc.sasc.biopet.extensions.
{
Cat
,
Raxml
,
RunGubbins
}
import
nl.lumc.sasc.biopet.pipelines.shiva.Shiva
import
nl.lumc.sasc.biopet.pipelines.shiva.
{
Shiva
,
ShivaReport
}
import
nl.lumc.sasc.biopet.extensions.tools.BastyGenerateFasta
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -51,6 +52,13 @@ class Basty(val parent: Configurable) extends QScript with MultiSampleQScript {
lazy
val
shiva
=
new
Shiva
(
qscript
)
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
shiva
=
new
ShivaReport
(
this
)
shiva
.
outputDir
=
new
File
(
outputDir
,
"report"
)
shiva
.
summaryDbFile
=
summaryDbFile
Some
(
shiva
)
}
def
summaryFiles
:
Map
[
String
,
File
]
=
Map
()
def
summarySettings
:
Map
[
String
,
Any
]
=
Map
(
"boot_runs"
->
numBoot
)
...
...
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