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biopet.biopet
Commits
8c75f931
Commit
8c75f931
authored
Mar 04, 2016
by
Wai Yi Leung
Browse files
Merge branch 'fix-basecounter_executable' into 'develop'
Fix basecounter executable See merge request !341
parents
b3e8c237
be7e4e74
Changes
2
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public/biopet-tools-package/src/main/scala/nl/lumc/sasc/biopet/BiopetToolsExecutable.scala
View file @
8c75f931
...
...
@@ -31,6 +31,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfToTsv
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfFilter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
VcfStats
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
BaseCounter
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FindRepeatsPacBio
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
MpileupToVcf
,
nl
.
lumc
.
sasc
.
biopet
.
tools
.
FastqSplitter
,
...
...
public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
8c75f931
...
...
@@ -104,7 +104,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)),
Map
()))
else
Nil
)
++
List
(
"Files"
->
filesPage
),
List
(
),
List
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"showPlot"
->
true
)),
"Preprocessing"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
Map
(
"sampleLevel"
->
true
)))
++
...
...
@@ -122,10 +122,10 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
)
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
),
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
Map
()))
else
Nil
),
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
::
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
))
...
...
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