Skip to content
GitLab
Projects
Groups
Snippets
Help
Loading...
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
B
biopet.biopet
Project overview
Project overview
Details
Activity
Releases
Repository
Repository
Files
Commits
Branches
Tags
Contributors
Graph
Compare
CI / CD
CI / CD
Pipelines
Jobs
Schedules
Operations
Operations
Environments
Analytics
Analytics
CI / CD
Repository
Value Stream
Members
Members
Collapse sidebar
Close sidebar
Activity
Graph
Jobs
Commits
Open sidebar
Mirrors
biopet.biopet
Commits
e5b7192d
Commit
e5b7192d
authored
Aug 01, 2017
by
Vorderman
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Defutured covstats.ssp
parent
e2e3d2a5
Changes
7
Show whitespace changes
Inline
Side-by-side
Showing
7 changed files
with
485 additions
and
318 deletions
+485
-318
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+4
-5
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
+1
-0
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
...c/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+59
-42
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
...sc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
+82
-18
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+26
-26
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
+3
-3
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
...c/biopet/pipelines/mapping/MultisampleMappingReport.scala
+310
-224
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @
e5b7192d
...
...
@@ -7,6 +7,7 @@
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(nl.lumc.sasc.biopet.utils.summary.db.Schema)
#import(java.io.File)
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] %>
...
...
@@ -16,16 +17,14 @@
<%@ var target: Option[String] %>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("mean", "median", "max", "horizontal", "frac_min_10x", "frac_min_20x", "frac_min_30x", "frac_min_40x", "frac_min_50x") %>
<%@ var plotFile: Option[Schema.File] %>
<%@ var values: Map[String, Option[Any]] %>
#{
val moduleName = target.get + "_cov_stats"
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val plotFile = Await.result(summary.getFile(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), "plot"), Duration.Inf)
val originalPlot = new File(plotFile.get.path)
val plot = new File(outputDir, target.get + "_cov_stats.png")
val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), sampleId.map(SampleId).get, libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
if (originalPlot.exists()) IoUtils.copyFile(originalPlot, plot)
}#
<img src="${plot.getName}">
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp
View file @
e5b7192d
...
...
@@ -85,6 +85,7 @@
#for (field <- fields)
<td>${results(field)}</td>
#end
#end
</tr>
#end
#end
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
View file @
e5b7192d
...
...
@@ -23,13 +23,11 @@ import nl.lumc.sasc.biopet.core.report.{
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
import
nl.lumc.sasc.biopet.utils.ConfigUtils
import
nl.lumc.sasc.biopet.utils.rscript.
{
LinePlot
,
StackedBarPlot
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import
nl.lumc.sasc.biopet.utils.summary.db.Schema._
import
scala.collection.mutable.ArrayBuffer
import
scala.concurrent.
{
Await
,
Future
}
...
...
@@ -71,11 +69,20 @@ object BammetricsReport extends ReportBuilder {
)
}
/** Generates values for bamMetricsPage */
def
bamMetricsPageValues
(
summary
:
SummaryDb
,
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
metricsTag
:
String
=
"bammetrics"
)
:
Map
[
String
,
Any
]
=
{
Map
(
""
->
""
)
}
/** Generates a page with alignment stats */
def
bamMetricsPage
(
summary
:
SummaryDb
,
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
Future
{
metricsTag
:
String
=
"bammetrics"
)
:
Future
[
ReportPage
]
=
{
val
wgsExecuted
=
summary
.
getStatsSize
(
runId
,
metricsTag
,
"wgs"
,
...
...
@@ -115,6 +122,15 @@ object BammetricsReport extends ReportBuilder {
case
_
=>
Nil
}
val
covstatsPlotValuesArray
=
ArrayBuffer
[(
String
,
Map
[
String
,
Any
])]()
for
(
t
<-
targets
)
{
covstatsPlotValuesArray
+=
Tuple2
(
t
,
BammetricsReportPage
.
covstatsPlotValues
(
summary
,
runId
,
sampleId
,
libId
,
Some
(
t
)))
}
val
covstatsPlotValuesList
=
covstatsPlotValuesArray
.
toList
Future
{
ReportPage
(
if
(
targets
.
isEmpty
)
List
()
else
...
...
@@ -122,9 +138,9 @@ object BammetricsReport extends ReportBuilder {
"Targets"
->
Future
.
successful
(
ReportPage
(
List
(),
targets
.
map
(
t
=>
t
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
Map
(
"target"
->
Some
(
t
))
)),
covstatsPlotValuesList
.
map
(
covstats
=>
covstats
.
_1
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
covstats
.
_2
)),
Map
()))),
List
(
"Summary"
->
ReportSection
(
...
...
@@ -155,6 +171,7 @@ object BammetricsReport extends ReportBuilder {
Map
(
"metricsTag"
->
metricsTag
)
)
}
}
/**
* Generates the lines for alignmentSummaryPlot
...
...
bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReportPage.scala
View file @
e5b7192d
...
...
@@ -2,10 +2,14 @@ package nl.lumc.sasc.biopet.pipelines.bammetrics
import
nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport.mappingQualityPlotTables
import
nl.lumc.sasc.biopet.utils.summary.db.Schema.
{
Library
,
Sample
}
import
nl.lumc.sasc.biopet.utils.summary.db.
SummaryDb
import
nl.lumc.sasc.biopet.utils.summary.db.
{
Schema
,
SummaryDb
}
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import
scala.concurrent.Await
import
scala.concurrent.duration.Duration
import
java.io.File
object
BammetricsReportPage
{
def
alignmentSummaryValues
(
summary
:
SummaryDb
,
runId
:
Int
,
...
...
@@ -99,7 +103,8 @@ object BammetricsReportPage {
else
None
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"clipping"
,
"general"
,
x
)).
toMap
val
clippingTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"bamstats"
,
sampleId
,
statsPaths
)
val
clippingTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"bamstats"
,
sampleId
,
statsPaths
)
Map
(
"clippingPlotTables"
->
clippingPlotTables
,
"clippingTableResults"
->
clippingTableResults
,
...
...
@@ -117,7 +122,8 @@ object BammetricsReportPage {
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
fields
:
List
[
String
]
=
List
(
"mean_insert_size"
,
"standard_deviation"
,
"median_insert_size"
),
fields
:
List
[
String
]
=
List
(
"mean_insert_size"
,
"standard_deviation"
,
"median_insert_size"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
...
...
@@ -133,7 +139,11 @@ object BammetricsReportPage {
else
None
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"metrics"
,
x
.
toUpperCase
)).
toMap
val
insertSizeTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"CollectInsertSizeMetrics"
,
sampleId
,
statsPaths
)
val
insertSizeTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"CollectInsertSizeMetrics"
,
sampleId
,
statsPaths
)
Map
(
"insertSizePlotTables"
->
insertSizePlotTables
,
"insertSizeTableResults"
->
insertSizeTableResults
,
...
...
@@ -150,7 +160,10 @@ object BammetricsReportPage {
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
fields
:
List
[
String
]
=
List
(
"PF_ALIGNED_BASES"
,
"MEDIAN_5PRIME_BIAS"
,
"MEDIAN_3PRIME_BIAS"
,
"MEDIAN_5PRIME_TO_3PRIME_BIAS"
),
fields
:
List
[
String
]
=
List
(
"PF_ALIGNED_BASES"
,
"MEDIAN_5PRIME_BIAS"
,
"MEDIAN_3PRIME_BIAS"
,
"MEDIAN_5PRIME_TO_3PRIME_BIAS"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
...
...
@@ -166,7 +179,8 @@ object BammetricsReportPage {
else
None
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"metrics"
,
x
.
toUpperCase
)).
toMap
val
rnaHistogramTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"rna"
,
sampleId
,
statsPaths
)
val
rnaHistogramTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"rna"
,
sampleId
,
statsPaths
)
Map
(
"rnaHistogramPlotTables"
->
rnaHistogramPlotTables
,
"rnaHistogramTableResults"
->
rnaHistogramTableResults
,
...
...
@@ -183,7 +197,20 @@ object BammetricsReportPage {
allLibraries
:
Seq
[
Library
],
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
fields
:
List
[
String
]
=
List
(
"mean_coverage"
,
"pct_5x"
,
"pct_10x"
,
"pct_15x"
,
"pct_20x"
,
"pct_25x"
,
"pct_30x"
,
"pct_40x"
,
"pct_50x"
,
"pct_60x"
,
"pct_70x"
,
"pct_80x"
,
"pct_90x"
,
"pct_100x"
),
fields
:
List
[
String
]
=
List
(
"mean_coverage"
,
"pct_5x"
,
"pct_10x"
,
"pct_15x"
,
"pct_20x"
,
"pct_25x"
,
"pct_30x"
,
"pct_40x"
,
"pct_50x"
,
"pct_60x"
,
"pct_70x"
,
"pct_80x"
,
"pct_90x"
,
"pct_100x"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
...
...
@@ -199,7 +226,8 @@ object BammetricsReportPage {
else
None
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"metrics"
,
x
.
toUpperCase
)).
toMap
val
wgsHistogramTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"wgs"
,
sampleId
,
statsPaths
)
val
wgsHistogramTableResults
=
summary
.
getStatsForLibraries
(
runId
,
"bammetrics"
,
"wgs"
,
sampleId
,
statsPaths
)
Map
(
"wgsHistogramPlotTables"
->
wgsHistogramPlotTables
,
"wgsHistogramTableResults"
->
wgsHistogramTableResults
,
...
...
@@ -210,5 +238,41 @@ object BammetricsReportPage {
"libId"
->
libId
)
}
def
covstatsPlotValues
(
summary
:
SummaryDb
,
runId
:
Int
,
sampleId
:
Option
[
Int
],
libId
:
Option
[
Int
],
target
:
Option
[
String
],
metricsTag
:
String
=
"bammetrics"
,
fields
:
List
[
String
]
=
List
(
"mean"
,
"median"
,
"max"
,
"horizontal"
,
"frac_min_10x"
,
"frac_min_20x"
,
"frac_min_30x"
,
"frac_min_40x"
,
"frac_min_50x"
))
:
Map
[
String
,
Any
]
=
{
val
moduleName
=
target
.
get
+
"_cov_stats"
val
plotFile
:
Option
[
Schema.File
]
=
Await
.
result
(
summary
.
getFile
(
runId
,
PipelineName
(
metricsTag
),
ModuleName
(
moduleName
),
sampleId
.
map
(
SampleId
).
get
,
libId
.
map
(
LibraryId
).
getOrElse
(
NoLibrary
),
"plot"
),
Duration
.
Inf
)
val
statsPaths
=
fields
.
map
(
x
=>
x
->
List
(
"coverage"
,
"_all"
,
x
)).
toMap
val
values
:
Map
[
String
,
Option
[
Any
]]
=
summary
.
getStatKeys
(
runId
,
PipelineName
(
metricsTag
),
ModuleName
(
moduleName
),
sampleId
.
map
(
SampleId
).
get
,
libId
.
map
(
LibraryId
).
getOrElse
(
NoLibrary
),
statsPaths
)
Map
(
"plotFile"
->
plotFile
,
"values"
->
values
,
"target"
->
target
,
"metricsTag"
->
metricsTag
)
}
}
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
e5b7192d
...
...
@@ -53,15 +53,16 @@ object FlexiprepReport extends ReportBuilder {
/** Index page for a flexiprep report */
def
indexPage
:
Future
[
ReportPage
]
=
{
val
flexiprepPageSummaries
=
this
.
flexiprepPageSummaries
(
summary
,
sampleId
.
get
,
libId
.
get
)
this
.
flexiprepPage
(
flexiprepPageSummaries
).
map
{
page
=>
this
.
flexiprepPage
(
flexiprepPageSummaries
).
map
{
page
=>
ReportPage
(
Nil
,
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
)
:::
page
.
sections
,
Map
())
}}
}
}
/** Generate a QC report page for 1 single library, sampleId and libId must be defined in the arguments */
def
flexiprepPageSummaries
(
summary
:
SummaryDb
,
sampleId
:
Int
,
...
...
@@ -73,7 +74,7 @@ object FlexiprepReport extends ReportBuilder {
sampleId
,
libId
,
multisample
=
false
)
val
flexiprepBaseSummary
:
Map
[
String
,
Any
]
=
FlexiprepBaseSummary
.
values
(
summary
,
val
flexiprepBaseSummary
:
Map
[
String
,
Any
]
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
...
...
@@ -81,8 +82,7 @@ object FlexiprepReport extends ReportBuilder {
libId
,
multisample
=
false
)
Map
(
"flexiprepReadSummary"
->
flexiprepReadSummary
,
"flexiprepBaseSummary"
->
flexiprepBaseSummary
)
"flexiprepBaseSummary"
->
flexiprepBaseSummary
)
}
def
flexiprepPage
(
summaries
:
Map
[
String
,
Map
[
String
,
Any
]])
:
Future
[
ReportPage
]
=
{
...
...
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @
e5b7192d
...
...
@@ -345,10 +345,10 @@ object GearsReport extends MultisampleReportBuilder {
val
flexiprepReportPage
=
if
(
flexiprepExecuted
)
{
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
Some
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
flexiprepPageSummaries
))
}
else
None
}
else
None
val
centrifugePageAllMappingsKronaPlot
=
GearsKronaPlot
.
values
(
summary
,
runId
,
...
...
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @
e5b7192d
...
...
@@ -14,9 +14,18 @@
*/
package
nl.lumc.sasc.biopet.pipelines.mapping
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.core.report.
{
MultisampleReportBuilder
,
ReportBuilderExtension
,
ReportPage
,
ReportSection
}
import
nl.lumc.sasc.biopet.pipelines.bammetrics.
{
BammetricsReport
,
BammetricsReportPage
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepReadSummary
,
FlexiprepBaseSummary
,
FlexiprepReport
}
import
nl.lumc.sasc.biopet.pipelines.flexiprep.
{
FlexiprepReadSummary
,
FlexiprepBaseSummary
,
FlexiprepReport
}
import
nl.lumc.sasc.biopet.pipelines.gears.GearsKronaPlot
import
nl.lumc.sasc.biopet.utils.config.Configurable
import
nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
...
...
@@ -137,16 +146,58 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
clippingReportValues
=
BammetricsReportPage
.
clippingValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
insertSizeReportValues
=
BammetricsReportPage
.
insertSizeValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
wgsHistogramReportValues
=
BammetricsReportPage
.
wgsHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
rnaHistogramReportValues
=
BammetricsReportPage
.
rnaHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
val
clippingReportValues
=
BammetricsReportPage
.
clippingValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
insertSizeReportValues
=
BammetricsReportPage
.
insertSizeValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
wgsHistogramReportValues
=
BammetricsReportPage
.
wgsHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
rnaHistogramReportValues
=
BammetricsReportPage
.
rnaHistogramValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
,
showTable
=
false
)
Future
{
ReportPage
(
List
(
"Samples"
->
generateSamplesPage
(
pageArgs
))
++
...
...
@@ -248,18 +299,49 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
summary
.
getStatsSize
(
runId
,
"flexiprep"
,
sample
=
sampleId
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
val
centrifugeAllMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
samples
,
libraries
,
sampleId
,
libId
,
Some
(
"centrifuge"
))
val
centrifugeUniqueMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_unique_report"
,
samples
,
libraries
,
sampleId
,
libId
)
val
dustbinAnalysisReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearskraken"
,
"krakenreport"
,
samples
,
libraries
,
sampleId
,
libId
)
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
preprocessingReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
centrifugeAllMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_report"
,
samples
,
libraries
,
sampleId
,
libId
,
Some
(
"centrifuge"
))
val
centrifugeUniqueMappingsReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearscentrifuge"
,
"centrifuge_unique_report"
,
samples
,
libraries
,
sampleId
,
libId
)
val
dustbinAnalysisReportValues
=
GearsKronaPlot
.
values
(
summary
,
runId
,
"gearskraken"
,
"krakenreport"
,
samples
,
libraries
,
sampleId
,
libId
)
val
alignmentSummaryReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
showPlot
=
true
)
val
preprocessingReportValues
=
BammetricsReportPage
.
alignmentSummaryValues
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
sampleLevel
=
true
)
val
flexiprepReadSummary
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
val
flexiprepBaseSummary
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
)
Future
{
ReportPage
(
...
...
@@ -268,7 +350,9 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(
"Non-unique"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"All mappings"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
...
...
@@ -286,7 +370,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
List
(
"Krona Plot"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
dustbinAnalysisReportValues
)),
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
,
dustbinAnalysisReportValues
)),
Map
())))
else
Nil
),
List
(
...
...
@@ -300,9 +385,11 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
(
if
(
flexiprepExecuted
)
List
(
"QC reads"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
flexiprepReadSummary
),
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"
,
flexiprepReadSummary
),
"QC bases"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
flexiprepBaseSummary
)
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp"
,
flexiprepBaseSummary
)
)
else
Nil
),
args
...
...
@@ -310,9 +397,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
}
/** Library page */
def
libraryPage
(
sampleId
:
Int
,
libId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
{
def
libraryPage
(
sampleId
:
Int
,
libId
:
Int
,
args
:
Map
[
String
,
Any
])
:
Future
[
ReportPage
]
=
{
val
krakenExecuted
=
Await
.
result
(
summary
.
getStatsSize
(
runId
,
"gearskraken"
,
"krakenreport"
,
...
...
@@ -332,12 +417,12 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
sample
=
sampleId
,
mustHaveLibrary
=
true
),
Duration
.
Inf
)
>=
1
val
flexiprepPageSummaries
=
FlexiprepReport
.
flexiprepPageSummaries
(
summary
,
sampleId
,
libId
)
Future
{
ReportPage
(
(
"Alignment"
->
BammetricsReport
.
bamMetricsPage
(
summary
,
Some
(
sampleId
),
Some
(
libId
)))
::
(
if
(
flexiprepExecuted
)
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
summary
,
sampleId
,
libId
))
List
(
"QC"
->
FlexiprepReport
.
flexiprepPage
(
flexiprepPageSummaries
))
else
Nil
)
:::
(
if
(
centrifugeExecuted
)
List
(
"Centrifuge analysis"
->
Future
.
successful
(
ReportPage
(
...
...
@@ -352,7 +437,8 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
Map
(
"summaryStatsTag"
->
"centrifuge_unique_report"
))),
Map
(
"summaryModuleTag"
->
"gearscentrifuge"
,
"centrifugeTag"
->
Some
(
"centrifuge"
))
)))
else
Nil
)
:::
(
if
(
krakenExecuted
)
else
Nil
)
:::
(
if
(
krakenExecuted
)
List
(
"Dustbin analysis"
->
Future
.
successful
(
ReportPage
(
List
(),
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment