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biopet.biopet
Commits
9034e179
Commit
9034e179
authored
Jan 12, 2016
by
Peter van 't Hof
Browse files
Fixed report types
parent
56766d98
Changes
7
Hide whitespace changes
Inline
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public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
View file @
9034e179
...
...
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import
java.io.File
import
nl.lumc.sasc.biopet.core._
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import
nl.lumc.sasc.biopet.extensions.picard.BuildBamIndex
import
nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
...
...
@@ -95,7 +96,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
}
}
override
def
reportClass
=
{
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
carp
=
new
CarpReport
(
this
)
carp
.
outputDir
=
new
File
(
outputDir
,
"report"
)
carp
.
summaryFile
=
summaryFile
...
...
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
View file @
9034e179
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.carp
import
nl.lumc.sasc.biopet.core.report.
{
ReportSection
,
ReportBuilderExtension
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportSection
,
ReportBuilderExtension
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
View file @
9034e179
...
...
@@ -15,7 +15,7 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gentrap
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
9034e179
package
nl.lumc.sasc.biopet.pipelines.mapping
import
nl.lumc.sasc.biopet.core.report.
{
ReportBuilderExtension
,
ReportSection
,
ReportPage
,
MultisampleReportBuilder
}
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
nl.lumc.sasc.biopet.utils.config.Configurable
/**
* Created by pjvanthof on 11/01/16.
*/
* Created by pjvanthof on 11/01/16.
*/
class
MultisampleMappingReport
(
val
root
:
Configurable
)
extends
ReportBuilderExtension
{
def
builder
=
MultisampleMappingReport
}
...
...
@@ -57,8 +57,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"After QC fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"
),
"Bam files per lib"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"
,
Map
(
"sampleLevel"
->
false
)),
"Preprocessed bam files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp"
,
Map
(
"pipelineName"
->
"shiva"
,
"fileTag"
->
"preProcessBam"
)))
,
Map
())
Map
(
"pipelineName"
->
"shiva"
,
"fileTag"
->
"preProcessBam"
))),
Map
())
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
View file @
9034e179
...
...
@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import
java.io.File
import
htsjdk.samtools.SamReaderFactory
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.core.
{
PipelineCommand
,
Reference
,
MultiSampleQScript
}
import
nl.lumc.sasc.biopet.extensions.Ln
import
nl.lumc.sasc.biopet.extensions.picard.
{
MarkDuplicates
,
MergeSamFiles
,
AddOrReplaceReadGroups
,
SamToFastq
}
...
...
@@ -37,7 +38,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
addSummaryJobs
()
}
override
def
reportClass
=
{
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
report
=
new
MultisampleMappingReport
(
this
)
report
.
outputDir
=
new
File
(
outputDir
,
"report"
)
report
.
summaryFile
=
summaryFile
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
9034e179
...
...
@@ -15,13 +15,13 @@
*/
package
nl.lumc.sasc.biopet.pipelines.shiva
import
java.io.
{
File
,
PrintWriter
}
import
java.io.
{
File
,
PrintWriter
}
import
nl.lumc.sasc.biopet.core.report._
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import
nl.lumc.sasc.biopet.utils.summary.
{
Summary
,
SummaryValue
}
import
nl.lumc.sasc.biopet.utils.summary.
{
Summary
,
SummaryValue
}
/**
* With this extension the report is executed within a pipeline
...
...
@@ -100,7 +100,8 @@ object ShivaReport extends MultisampleMappingReportTrait {
/** Files page, can be used general or at sample level */
override
def
filesPage
:
ReportPage
=
{
val
vcfFilesSection
=
if
(
variantcallingExecuted
)
List
(
"VCF files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp"
,
Map
(
"sampleId"
->
None
)))
else
Nil
Map
(
"sampleId"
->
None
)))
else
Nil
val
oldPage
=
super
.
filesPage
oldPage
.
copy
(
sections
=
oldPage
.
sections
++
vcfFilesSection
)
}
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @
9034e179
...
...
@@ -16,8 +16,9 @@
package
nl.lumc.sasc.biopet.pipelines.shiva
import
nl.lumc.sasc.biopet.core.Reference
import
nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import
nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
import
nl.lumc.sasc.biopet.pipelines.mapping.
{
MultisampleMappingTrait
}
import
nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import
nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import
org.broadinstitute.gatk.queue.QScript
...
...
@@ -28,7 +29,7 @@ import org.broadinstitute.gatk.queue.QScript
*/
trait
ShivaTrait
extends
MultisampleMappingTrait
with
Reference
with
TargetRegions
{
qscript
:
QScript
=>
override
def
reportClass
=
{
override
def
reportClass
:
Option
[
ReportBuilderExtension
]
=
{
val
shiva
=
new
ShivaReport
(
this
)
shiva
.
outputDir
=
new
File
(
outputDir
,
"report"
)
shiva
.
summaryFile
=
summaryFile
...
...
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