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biopet.biopet
Commits
f069ee1e
Commit
f069ee1e
authored
Feb 08, 2016
by
Peter van 't Hof
Browse files
Hide insertsize plot on single end runs
parent
a5bf52fd
Changes
2
Hide whitespace changes
Inline
Side-by-side
public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
f069ee1e
...
...
@@ -61,6 +61,8 @@ object BammetricsReport extends ReportBuilder {
val
wgsExecuted
=
summary
.
getValue
(
sampleId
,
libId
,
metricsTag
,
"stats"
,
"wgs"
).
isDefined
val
rnaExecuted
=
summary
.
getValue
(
sampleId
,
libId
,
metricsTag
,
"stats"
,
"rna"
).
isDefined
val
insertsizeMetrics
=
summary
.
getValue
(
sampleId
,
libId
,
metricsTag
,
"stats"
,
"CollectInsertSizeMetrics"
,
"metrics"
).
isDefined
val
targets
=
(
summary
.
getValue
(
sampleId
,
libId
,
metricsTag
,
"settings"
,
"amplicon_name"
),
summary
.
getValue
(
sampleId
,
libId
,
metricsTag
,
"settings"
,
"roi_name"
)
...
...
@@ -77,9 +79,9 @@ object BammetricsReport extends ReportBuilder {
targets
.
map
(
t
=>
t
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
Map
(
"target"
->
Some
(
t
)))),
Map
())),
List
(
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
,
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"showPlot"
->
true
))
)
++
(
if
(
wgsExecuted
)
List
(
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
)
++
(
if
(
insertsizeMetrics
)
List
(
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"showPlot"
->
true
))
)
else
Nil
)
++
(
if
(
wgsExecuted
)
List
(
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
Map
(
"showPlot"
->
true
)))
else
Nil
)
++
(
if
(
rnaExecuted
)
List
(
"Rna coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp"
,
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
f069ee1e
...
...
@@ -28,6 +28,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
val
wgsExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"wgs"
).
values
.
exists
(
_
.
isDefined
)
val
rnaExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"rna"
).
values
.
exists
(
_
.
isDefined
)
val
insertsizeExecuted
=
summary
.
getSampleValues
(
"bammetrics"
,
"stats"
,
"CollectInsertSizeMetrics"
,
"metrics"
).
values
.
exists
(
_
.
isDefined
)
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
exists
{
case
((
sample
,
lib
),
value
)
=>
value
.
isDefined
}
...
...
@@ -44,9 +45,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Report"
->
frontSection
,
"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
)))
++
)
)
++
(
if
(
insertsizeExecuted
)
List
(
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
++
(
if
(
wgsExecuted
)
List
(
"Whole genome coverage"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)))
else
Nil
)
++
...
...
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