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biopet.biopet
Commits
81d36084
Commit
81d36084
authored
Jan 12, 2016
by
Peter van 't Hof
Browse files
Fix reference tag
parent
189a25d4
Changes
4
Hide whitespace changes
Inline
Side-by-side
public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
View file @
81d36084
...
...
@@ -32,4 +32,6 @@ object CarpReport extends MultisampleMappingReportTrait {
/** Name of the report */
def
reportName
=
"Carp Report"
override
def
frontSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"
)
override
def
pipelineName
=
"carp"
}
\ No newline at end of file
public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
View file @
81d36084
...
...
@@ -34,4 +34,6 @@ object GentrapReport extends MultisampleMappingReportTrait {
/** Name of the report */
def
reportName
=
"Gentrap Report"
override
def
pipelineName
=
"gentrap"
}
\ No newline at end of file
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
81d36084
...
...
@@ -21,20 +21,21 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
/** Front section for the report */
def
frontSection
:
ReportSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp"
)
def
pipelineName
=
"multisamplemapping"
/** 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
(
"Reference"
->
ReportPage
(
List
(),
List
(
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
"shiva"
))
"Reference"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/reference.ssp"
,
Map
(
"pipeline"
->
pipelineName
))
),
Map
()),
"Files"
->
filesPage
,
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
())
),
List
(
"Report"
->
Repor
tSection
(
"/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"
)
,
"Report"
->
fron
tSection
,
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
),
...
...
@@ -57,7 +58,7 @@ 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"
->
pipelineName
,
"fileTag"
->
"preProcessBam"
))),
Map
())
/** Single sample page */
def
samplePage
(
sampleId
:
String
,
args
:
Map
[
String
,
Any
])
:
ReportPage
=
{
...
...
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
81d36084
...
...
@@ -42,6 +42,8 @@ object ShivaReport extends MultisampleMappingReportTrait {
override
def
frontSection
=
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"
)
override
def
pipelineName
=
"shiva"
override
def
extFiles
=
super
.
extFiles
++
List
(
"js/gears.js"
)
.
map
(
x
=>
ExtFile
(
"/nl/lumc/sasc/biopet/pipelines/gears/report/ext/"
+
x
,
x
))
...
...
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