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biopet.biopet
Commits
200da965
Commit
200da965
authored
Mar 07, 2017
by
Peter van 't Hof
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Fixed flexiprep report
parent
99c245a2
Changes
4
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4 changed files
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22 additions
and
14 deletions
+22
-14
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
+1
-1
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
...l/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
+17
-10
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
.../sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
+1
-1
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
...umc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
+3
-2
No files found.
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp
View file @
200da965
...
...
@@ -122,7 +122,7 @@
#if (multisample)
<a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
#else
${sample}
${sample
.name
}
#end
</td>
#for (lib <- libraries.filter(_.sampleId == sample.id))
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp
View file @
200da965
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var sampleId: Option[String] %>
<%@ var libId: Option[String] %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Flexiprep</td></tr>
<tr><th>Version</th><td>${
summary.getValue("meta", "pipeline_
version
")
}</td></tr>
<tr><th>Last commit hash</th><td>${
summary.getValue("meta", "last_
commit
_h
ash
")
}</td></tr>
<tr><th>Output directory</th><td>${
summary.getValue("meta", "output_dir")
}</td></tr>
<tr><th>Sample ID</th><td>${
sampleId
}</td></tr>
<tr><th>Library ID</th><td>${
libId
}</td></tr>
<tr><th>Version</th><td>${
run.
version}</td></tr>
<tr><th>Last commit hash</th><td>${
run.
commit
H
ash}</td></tr>
<tr><th>Output directory</th><td>${
run.outputDir
}</td></tr>
<tr><th>Sample ID</th><td>${
Await.result(summary.getSampleName(sampleId.get), Duration.Inf)
}</td></tr>
<tr><th>Library ID</th><td>${
Await.result(summary.getLibraryName(libId.get), Duration.Inf)
}</td></tr>
</tbody>
</table>
<br/>
...
...
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp
View file @
200da965
...
...
@@ -127,7 +127,7 @@
#if (multisample)
<a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a>
#else
${sample}
${sample
.name
}
#end
</td>
#for (lib <- libraries.filter(_.sampleId == sample.id))
...
...
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @
200da965
...
...
@@ -45,8 +45,9 @@ object FlexiprepReport extends ReportBuilder {
ReportPage
(
List
(
"Versions"
->
ReportPage
(
List
(),
List
(
"Executables"
->
ReportSection
(
"/nl/lumc/sasc/biopet/core/report/executables.ssp"
)),
Map
()),
"Files"
->
ReportPage
(
List
(),
List
(
"Input fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"
),
"After QC fastq files"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"
)
//TODO: Fix files
// "Input fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp"),
// "After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp")
),
Map
())
),
List
(
"Report"
->
ReportSection
(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp"
)
...
...
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