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biopet.biopet
Commits
b5859840
Commit
b5859840
authored
Mar 01, 2017
by
Peter van 't Hof
Browse files
Fixing insertsize templates
parent
55952ce4
Changes
2
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Inline
Side-by-side
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp
View file @
b5859840
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.
db.
Summary
Db
)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
#import(nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport)
#import(java.io.File)
#import(org.apache.commons.io.FileUtils)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var sampleLevel: Boolean = false %>
...
...
@@ -14,13 +15,9 @@
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
#{
val samples = sampleId match {
case Some(sample) => {
List(sample.toString)
}
case _ => summary.samples.toList
}
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
}#
#if (showIntro)
...
...
@@ -72,28 +69,27 @@
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(
""
)
case (Some(
libId
), _) => List(libId
.toString
)
case _ => summary.
l
ibraries(sample).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(
None
)
case (Some(
_
), _) => List(libId)
case _ =>
Await.result(
summary.
getL
ibraries(sample
Id = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#{ val libName = libId.map(l => Await.result(summary.getLibraryName(l), Duration.Inf)) }#
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
val fieldValues = for (field <- fields) yield {
summary.getValue((prefixPath ::: List("CollectInsertSizeMetrics", "metrics", field.toUpperCase)):_*).getOrElse("N/A")
}
}#
#for (value <- fieldValues)
<td>${value}</td>
#end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample.name}/Libraries/${libName}/index.html">${libName}</a></td> #end
#{
val statsPaths = fields.map(x => x -> List("mapping_quality", "general", x)).toMap
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
}#
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
</tr>
#end
#end
...
...
biopet-extensions/src/main/scala/nl/lumc/sasc/biopet/extensions/picard/CollectMultipleMetrics.scala
View file @
b5859840
...
...
@@ -99,7 +99,7 @@ class CollectMultipleMetrics(val parent: Configurable) extends Picard with Summa
case
_
if
p
==
Programs
.
CollectAlignmentSummaryMetrics
.
toString
=>
qscript
.
addSummarizable
(
summarizable
(()
=>
Picard
.
getMetrics
(
new
File
(
outputName
+
".alignment_summary_metrics"
),
groupBy
=
Some
(
"CATEGORY"
))),
p
,
forceSingle
=
true
)
case
_
if
p
==
Programs
.
CollectInsertSizeMetrics
.
toString
=>
qscript
.
addSummarizable
(
summarizable
(()
=>
if
(
!
new
File
(
outputName
+
".insert_size_metrics"
).
exists
())
Map
(
qscript
.
addSummarizable
(
summarizable
(()
=>
if
(
new
File
(
outputName
+
".insert_size_metrics"
).
exists
())
Map
(
"metrics"
->
Picard
.
getMetrics
(
new
File
(
outputName
+
".insert_size_metrics"
)),
"histogram"
->
Picard
.
getHistogram
(
new
File
(
outputName
+
".insert_size_metrics"
))
)
...
...
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