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
91336909
Commit
91336909
authored
Mar 14, 2017
by
Peter van 't Hof
Browse files
Options
Browse Files
Download
Email Patches
Plain Diff
Fixing BIOPET-542 and BIOPET-615
parent
a085648e
Changes
3
Hide whitespace changes
Inline
Side-by-side
Showing
3 changed files
with
56 additions
and
69 deletions
+56
-69
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
...c/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
+29
-39
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
...nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
+24
-28
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
...ala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+3
-2
No files found.
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsMultiTable.ssp
View file @
91336909
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#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)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = true %>
<%@ var
rootPath: String
%>
<%@ var
libId: Option[Int] = None
%>
<%@ var outputDir: File %>
<%@ var rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ 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") %>
#{
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)
}#
<table class="table">
<thead><tr>
<th>sample</th>
<th>mean</th>
<th>median</th>
<th>max</th>
<th>horizontal</th>
<th>frac min 10x</th>
<th>frac min 20x</th>
<th>frac min 30x</th>
<th>frac min 40x</th>
<th>frac min 50x</th>
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
#for (sample <- samples.
toList.sorted
)
#for (sample <- samples.
sortBy(_.name)
)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List(""
)
case (Some(libId), _) => List(libId.toString
)
case _ => summary.libraries(sample
).toList
val libs
: List[Option[Int]]
= (libId, sampleLevel) match {
case (_, true) => List(None
)
case (Some(_), _) => List(libId
)
case _ => Await.result(summary.getLibraries(sampleId = Some(sample.id), runId = Some(runId)), Duration.Inf).map(x => Some(x.id)
).toList
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
}/index.html">${sampl
e}</a></td>
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample
.name}/index.html">${sample.nam
e}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#if (!sampleLevel) <td><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td> #end
#{
val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List(metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
val total = summary.getValue((prefixPath ::: List("biopet_flagstat", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("biopet_flagstat", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("biopet_flagstat", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val moduleName = target.get + "_cov_stats"
val statsPaths = fields.map(x => x -> List("coverage", "_all", x)).toMap
val values = summary.getStatKeys(runId, PipelineName(metricsTag), ModuleName(moduleName), SampleId(sample.id), libId.map(LibraryId).getOrElse(NoLibrary), statsPaths)
}#
<td>${summary.getValue((prefixPath ::: "mean" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "median" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "max" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "horizontal" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_10x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_20x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_30x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_40x" :: Nil):_*)}</td>
<td>${summary.getValue((prefixPath ::: "frac_min_50x" :: Nil):_*)}</td>
#for (field <- fields)
<th>${values(field)}</th>
#end
</tr>
#end
#end
...
...
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/covstatsPlot.ssp
View file @
91336909
#import(nl.lumc.sasc.biopet.utils.IoUtils)
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(org.apache.commons.io.FileUtils)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#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)
<%@ var summary: Summary %>
<%@ var sampleId: Option[
String
] %>
<%@ var libId: Option[
String
] = None %>
<%@ var summary: Summary
Db
%>
<%@ var sampleId: Option[
Int
] %>
<%@ var libId: Option[
Int
] = None %>
<%@ var outputDir: File %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ 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") %>
#{
val originalPlot = new File(summary.getValue(sampleId, libId, metricsTag, "files", target.get + "_cov_stats", "plot", "path")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).toString)
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.getValue(sampleId, libId, metricsTag, "stats", target.get + "_cov_stats", "coverage", "_all")
.getOrElse(throw new IllegalArgumentException("No plot found in summary")).asInstanceOf[Map[String, Any]]
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}">
<table class="table">
<thead><tr>
<th>mean</th>
<th>median</th>
<th>max</th>
<th>horizontal</th>
<th>frac min 10x</th>
<th>frac min 20x</th>
<th>frac min 30x</th>
<th>frac min 40x</th>
<th>frac min 50x</th>
#for (field <- fields)
<th>${field}</th>
#end
</tr></thead>
<tbody>
<tr>
<td>${values.get("mean")}</td>
<td>${values.get("median")}</td>
<td>${values.get("max")}</td>
<td>${values.get("horizontal")}</td>
<td>${values.get("frac_min_10x")}</td>
<td>${values.get("frac_min_20x")}</td>
<td>${values.get("frac_min_30x")}</td>
<td>${values.get("frac_min_40x")}</td>
<td>${values.get("frac_min_50x")}</td>
#for (field <- fields)
<th>${values(field)}</th>
#end
</tr>
</tbody>
</table>
shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
View file @
91336909
...
...
@@ -66,8 +66,9 @@ trait ShivaReportTrait extends MultisampleMappingReportTrait {
/** Generate a page with all target coverage stats */
def
regionsPage
:
Option
[(
String
,
ReportPage
)]
=
{
val
roi
=
summary
.
getSetting
(
runId
,
"shiva"
).
get
(
"regions_of_interest"
)
val
amplicon
=
summary
.
getSetting
(
runId
,
"shiva"
).
get
(
"amplicon_bed"
)
val
shivaSettings
=
Await
.
result
(
summary
.
getSetting
(
runId
,
"shiva"
),
Duration
.
Inf
).
get
val
roi
=
shivaSettings
.
get
(
"regions_of_interest"
)
val
amplicon
=
shivaSettings
.
get
(
"amplicon_bed"
)
var
regionPages
:
Map
[
String
,
ReportPage
]
=
Map
()
...
...
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