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biopet.biopet
Commits
ffd2f2fa
Commit
ffd2f2fa
authored
Oct 27, 2015
by
Peter van 't Hof
Browse files
Hide variant report when multisample variantcalling is not executed
parent
6a776170
Changes
1
Hide whitespace changes
Inline
Side-by-side
public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
ffd2f2fa
...
...
@@ -36,6 +36,11 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
/** Object for report generation for Shiva pipeline */
object
ShivaReport
extends
MultisampleReportBuilder
{
def
variantcallingExecuted
=
summary
.
getValue
(
"shiva"
,
"settings"
,
"multisample_variantcalling"
)
match
{
case
true
=>
true
case
_
=>
false
}
/** Root page for the shiva report */
def
indexPage
=
{
val
regions
=
regionsPage
...
...
@@ -51,10 +56,10 @@ object ShivaReport extends MultisampleReportBuilder {
),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"
)
,
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
))
,
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp"
)
)
++
(
if
(
variantcallingExecuted
)
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
,
Map
(
"showPlot"
->
true
,
"showTable"
->
false
))
)
else
Nil
)
++
List
(
"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"
,
...
...
@@ -127,9 +132,9 @@ object ShivaReport extends MultisampleReportBuilder {
),
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
))
,
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
)
,
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"Preprocessing"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
))
)
++
(
if
(
variantcallingExecuted
)
List
(
"Variantcalling"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp"
)
)
else
Nil
)
++
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
),
args
)
}
...
...
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