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biopet.biopet
Commits
0da332ac
Commit
0da332ac
authored
Aug 23, 2016
by
Peter van 't Hof
Browse files
Removed insertsize plot on single end from report
parent
61896d06
Changes
2
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Inline
Side-by-side
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
View file @
0da332ac
...
...
@@ -126,6 +126,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
"skip_metrics"
->
skipMetrics
,
"skip_flexiprep"
->
skipFlexiprep
,
"skip_markduplicates"
->
skipMarkduplicates
,
"paired"
->
inputR2
.
isDefined
,
"aligner"
->
aligner
,
"chunking"
->
chunking
,
"number_of_chunks"
->
(
if
(
chunking
)
numberChunks
.
getOrElse
(
1
)
else
None
)
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
0da332ac
...
...
@@ -49,6 +49,7 @@ 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
(
_
!=
Some
(
None
))
val
pairedFound
=
summary
.
getLibraryValues
(
"mapping"
,
"settings"
,
"paired"
).
exists
(
_
.
_2
==
Some
(
true
))
val
flexiprepExecuted
=
summary
.
getLibraryValues
(
"flexiprep"
)
.
exists
{
case
((
sample
,
lib
),
value
)
=>
value
.
isDefined
}
...
...
@@ -71,7 +72,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
,
"showPlot"
->
true
,
"showTable"
->
false
)
))
++
(
if
(
insertsizeExecuted
)
List
(
"Insert Size"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp"
,
(
if
(
insertsizeExecuted
&&
pairedFound
)
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"
,
...
...
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