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biopet.biopet
Commits
c639a8b7
Commit
c639a8b7
authored
Aug 03, 2017
by
rhpvorderman
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Defutured MultiSampleMapping
parent
f7c21823
Changes
1
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1 changed file
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17 additions
and
9 deletions
+17
-9
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+17
-9
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mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
c639a8b7
...
@@ -342,11 +342,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
...
@@ -342,11 +342,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
flexiprepBaseSummary
=
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
bamMetricsReportValues
=
BammetricsReport
.
bamMetricsPageValues
(
summary
,
Some
(
sampleId
),
libId
)
Future
{
Future
{
ReportPage
(
ReportPage
(
List
(
"Libraries"
->
generateLibraryPage
(
args
),
List
(
"Libraries"
->
generateLibraryPage
(
args
),
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
None
))
++
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
bamMetricsReportValues
))
++
(
if
(
centrifugeExecuted
)
(
if
(
centrifugeExecuted
)
List
(
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
...
@@ -418,9 +419,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
...
@@ -418,9 +419,16 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
mustHaveLibrary
=
true
),
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
Duration
.
Inf
)
>=
1
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
val
bamMetricsReportValues
=
BammetricsReport
.
bamMetricsPageValues
(
summary
,
Some
(
sampleId
),
Some
(
libId
))
val
centrifugeAllMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
),
centrifugeTag
=
Some
(
"centrifuge"
))
val
centrifugeUniqueMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_unique_report"
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
),
centrifugeTag
=
Some
(
"centrifuge"
))
val
krakenDustbinAnalysisReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearskraken"
,
"krakenreport"
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
))
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
))
val
flexiprepReadSummaryReportValues
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
))
val
flexiprepBaseSummaryReportValues
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
Some
(
sampleId
),
Some
(
libId
))
Future
{
Future
{
ReportPage
(
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)
))
::
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
bamMetricsReportValues
))
::
(
if
(
flexiprepExecuted
)
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
flexiprepPageSummaries
))
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
flexiprepPageSummaries
))
else
Nil
)
:::
else
Nil
)
:::
...
@@ -430,12 +438,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
...
@@ -430,12 +438,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage
(
List
(),
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_report"
)
)),
centrifugeAllMappingsReportValues
)),
Map
()))),
Map
()))),
List
(
"Unique mappings"
->
ReportSection
(
List
(
"Unique mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
)
)),
centrifugeUniqueMappingsReportValues
)),
Map
(
"summary
ModuleTag
"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
Map
(
"summary
PipelineName
"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
)))
)))
else
else
Nil
)
:::
(
if
(
krakenExecuted
)
Nil
)
:::
(
if
(
krakenExecuted
)
...
@@ -443,17 +451,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
...
@@ -443,17 +451,17 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Dustbin analysis"
->
Future
.
successful
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)),
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
krakenDustbinAnalysisReportValues
)),
Map
())))
Map
())))
else
Nil
),
else
Nil
),
"Alignment"
->
ReportSection
(
"Alignment"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
)
::
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
,
alignmentSummaryReportValues
)
::
(
if
(
flexiprepExecuted
)
(
if
(
flexiprepExecuted
)
List
(
List
(
"QC reads"
->
ReportSection
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
),
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
flexiprepReadSummaryReportValues
),
"QC bases"
->
ReportSection
(
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
)
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
flexiprepBaseSummaryReportValues
)
)
)
else
Nil
),
else
Nil
),
args
args
...
...
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