Skip to content
GitLab
Projects
Groups
Snippets
/
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
Mirrors
biopet.biopet
Commits
56766d98
Commit
56766d98
authored
Jan 11, 2016
by
Peter van 't Hof
Browse files
Change gentrap report to multisample mapping report
parent
be731b74
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
View file @
56766d98
...
...
@@ -15,10 +15,9 @@
*/
package
nl.lumc.sasc.biopet.pipelines.gentrap
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
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
/**
* Class to generate report for [[Gentrap]]
...
...
@@ -29,68 +28,9 @@ class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
def
builder
=
GentrapReport
}
object
GentrapReport
extends
Multisample
ReportBuilder
{
object
GentrapReport
extends
Multisample
MappingReportTrait
{
/** Root page for the carp report */
def
indexPage
=
{
//Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
Map
(
"Files"
->
filesPage
,
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"
),
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
),
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)),
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
)),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
))
),
pageArgs
)
}
/** Files page, can be used general or at sample level */
def
filesPage
:
ReportPage
=
ReportPage
(
List
(),
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"
),
"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
())
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
),
"Files"
->
filesPage
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
if
(
summary
.
libraries
(
sampleId
).
size
>
1
)
Map
(
"showPlot"
->
true
)
else
Map
()),
"Preprocessing"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
)),
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
/** Library page */
def
libraryPage
(
sampleId
:
String
,
libId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
ReportPage
(
List
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)),
"QC"
->
FlexiprepReport
.
flexiprepPage
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
override
def
frontSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"
)
/** Name of the report */
def
reportName
=
"Gentrap Report"
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
56766d98
...
...
@@ -15,15 +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.core.report._
import
nl.lumc.sasc.biopet.utils.summary.
{
Summary
,
SummaryValue
}
import
nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
import
nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
import
nl.lumc.sasc.biopet.utils.summary.
{
Summary
,
SummaryValue
}
/**
* With this extension the report is executed within a pipeline
...
...
Write
Preview
Supports
Markdown
0%
Try again
or
attach a new file
.
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment