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biopet.biopet
Commits
e5b7192d
Commit
e5b7192d
authored
Aug 01, 2017
by
Ruben Vorderman
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Defutured covstats.ssp
parent
e2e3d2a5
Changes
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7 changed files
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485 additions
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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] %>
...
...
@@ -16,17 +17,15 @@
<%@ 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)
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"
,
...
...
@@ -115,45 +122,55 @@ object BammetricsReport extends ReportBuilder {
case
_
=>
Nil
}
ReportPage
(
if
(
targets
.
isEmpty
)
List
()
else
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
List
(
"Targets"
->
Future
.
successful
(
ReportPage
(
List
(),
covstatsPlotValuesList
.
map
(
covstats
=>
covstats
.
_1
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp"
,
covstats
.
_2
)),
Map
()))),
List
(
"Targets"
->
Future
.
successful
(
ReportPage
(
List
(),
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"
),
"Mapping Quality"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp"
,
Map
(
"showPlot"
->
true
)),
"Clipping"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp"
,
Map
(
"showPlot"
->
true
))
)
++
(
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"
,
Map
(
"showPlot"
->
true
)))
else
Nil
),
Map
(
"metricsTag"
->
metricsTag
)
)
"Summary"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"
),
"Mapping Quality"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp"
,
Map
(
"showPlot"
->
true
)),
"Clipping"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp"
,
Map
(
"showPlot"
->
true
))
)
++
(
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"
,
Map
(
"showPlot"
->
true
)))
else
Nil
),
Map
(
"metricsTag"
->
metricsTag
)
)
}
}
/**
...
...
@@ -541,4 +558,4 @@ object BammetricsReport extends ReportBuilder {
}
writer
.
close
()
}
}
\ No newline at end of file
}
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
,
...
...
@@ -145,16 +155,19 @@ object BammetricsReportPage {
)
}
def
rnaHistogramValues
(
summary
:
SummaryDb
,
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
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"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
runId
:
Int
,
allSamples
:
Seq
[
Sample
],
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"
),
sampleLevel
:
Boolean
=
false
,
showPlot
:
Boolean
=
false
,
showIntro
:
Boolean
=
true
,
showTable
:
Boolean
=
true
)
:
Map
[
String
,
Any
]
=
{
val
samples
=
sampleId
match
{
case
Some
(
id
)
=>
allSamples
.
filter
(
_
.
id
==
id
).
toList
...
...
@@ -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
...
...
@@ -53,36 +53,36 @@ 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
=>
ReportPage
(
Nil
,
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
)
:::
page
.
sections
,
Map
())
}}
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
,
libId
:
Int
)
:
Map
[
String
,
Map
[
String
,
Any
]]
=
{
sampleId
:
Int
,
libId
:
Int
)
:
Map
[
String
,
Map
[
String
,
Any
]]
=
{
val
flexiprepReadSummary
:
Map
[
String
,
Any
]
=
FlexiprepReadSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
multisample
=
false
)
val
flexiprepBaseSummary
:
Map
[
String
,
Any
]
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
libId
,
multisample
=
false
)
runId
,
samples
,
libraries
,
sampleId
,
libId
,
multisample
=
false
)
val
flexiprepBaseSummary
:
Map
[
String
,
Any
]
=
FlexiprepBaseSummary
.
values
(
summary
,
runId
,
samples
,
libraries
,
sampleId
,
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
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