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biopet.biopet
Commits
d030c0bf
Commit
d030c0bf
authored
Jun 25, 2015
by
Peter van 't Hof
Browse files
adding carp report to the pipeline
parent
d091609d
Changes
2
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public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
d030c0bf
...
...
@@ -40,7 +40,10 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
def
this
()
=
this
(
null
)
override
def
defaults
=
ConfigUtils
.
mergeMaps
(
Map
(
"mapping"
->
Map
(
"skip_markduplicates"
->
true
,
"aligner"
->
"bwa-mem"
)
"mapping"
->
Map
(
"skip_markduplicates"
->
true
,
"aligner"
->
"bwa-mem"
)
),
super
.
defaults
)
def
summaryFile
=
new
File
(
outputDir
,
"Carp.summary.json"
)
...
...
@@ -117,6 +120,13 @@ class Carp(val root: Configurable) extends QScript with MultiSampleQScript with
}
}
override
def
reportClass
=
{
val
carp
=
new
CarpReport
(
this
)
carp
.
outputDir
=
new
File
(
outputDir
,
"report"
)
carp
.
summaryFile
=
summaryFile
Some
(
carp
)
}
def
init
()
=
{
// ensure that no samples are called 'control' since that is our reserved keyword
require
(!
sampleIds
.
contains
(
"control"
),
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
View file @
d030c0bf
package
nl.lumc.sasc.biopet.pipelines.carp
import
nl.lumc.sasc.biopet.core.report.
{
ReportSection
,
ReportPage
,
MultisampleReportBuilder
}
import
nl.lumc.sasc.biopet.core.config.Configurable
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
,
ReportPage
,
MultisampleReportBuilder
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import
scala.io.Source
/**
* Created by pjvanthof on 25/06/15.
*/
class
CarpReport
{
class
CarpReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
val
builder
=
CarpReport
}
object
CarpReport
extends
MultisampleReportBuilder
{
...
...
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