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biopet.biopet
Commits
68751188
Commit
68751188
authored
Mar 29, 2017
by
Peter van 't Hof
Browse files
Removing unused templates
parent
9ab675f8
Changes
3
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flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepInputfiles.ssp
deleted
100644 → 0
View file @
9ab675f8
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
def removeDir(value: Option[Any]): Option[Any] = {
value.collect { case a =>
if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
else a
}
}
}#
<table class="table">
<thead><tr>
<th>Sample</th>
<th colspan="2">Library</th>
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString).sorted
case _ => summary.libraries(sample).toList.sorted
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
<td>${read}</td>
<td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "path"))}</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "input_" + read, "md5")}</td>
#end
</tr>
#end
#end
</tbody>
</table>
\ No newline at end of file
flexiprep/src/main/resources/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp
deleted
100644 → 0
View file @
9ab675f8
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport)
#import(java.io.File)
<%@ var summary: Summary %>
<%@ var sampleId: Option[String] = None %>
<%@ var libId: Option[String] = None %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
#{
val samples = sampleId match {
case Some(sample) => List(sample.toString)
case _ => summary.samples.toList
}
val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
def removeDir(value: Option[Any]): Option[Any] = {
value.collect { case a =>
if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
else a
}
}
}#
<table class="table">
<thead><tr>
<th>Sample</th>
<th colspan="2">Library</th>
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = libId match {
case Some(libId) => List(libId.toString).sorted
case _ => summary.libraries(sample).toList.sorted
}
val sampleRowspan = {
libs.size +
libs.count(summary.getLibraryValue(sample, _, "flexiprep", "settings", "paired").getOrElse(false) == true)
}
}#
<tr><td rowspan="${sampleRowspan}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td>
#for (libId <- libs)
#if (libs.head != libId) <tr> #end
#{ val paired = summary.getLibraryValue(sample, libId, "flexiprep", "settings", "paired").getOrElse(false) }#
<td #if (paired == true) rowspan="2" #end><a href="${rootPath}Samples/${sample}/Libraries/${libId}/index.html">${libId}</a></td>
#{ val reads = if (paired == true) List("R1", "R2") else List("R1") }#
#for (read <- reads)
#if (read == "R2") </tr><tr> #end
<td>${read}</td>
<td>${removeDir(summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "path"))}</td>
<td>${summary.getLibraryValue(sample, libId, "flexiprep", "files", "pipeline", "output_" + read, "md5")}</td>
#end
</tr>
#end
#end
</tbody>
</table>
\ No newline at end of file
shiva/src/main/resources/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp
deleted
100644 → 0
View file @
9ab675f8
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
#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 sampleLevel: Boolean = true %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
#{
val variantCallers = summary.getValue(sampleId, libId, "shivavariantcalling", "settings", "variantcallers").get.asInstanceOf[List[String]]
val pipelineOutputDir = summary.getValue("meta", "output_dir").getOrElse("").toString
def removeDir(value: Option[Any]): Option[Any] = {
value.collect { case a =>
if (a.toString.startsWith(pipelineOutputDir) && pipelineOutputDir.nonEmpty) "./" + a.toString.stripPrefix(pipelineOutputDir + File.separator)
else a
}
}
}#
<div class="panel-body">
<!-- Table -->
<table class="table">
<thead><tr>
<th>Variantcaller</th>
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
#if (variantCallers.size > 1)
<tr>
<td>Final (merged)</td>
<td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "path"))}</td>
<td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", "final", "md5")}</td>
</tr>
#end
#for (variantCaller <- variantCallers)
<tr>
<td>${variantCaller}</td>
<td>${removeDir(summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "path"))}</td>
<td>${summary.getValue(sampleId, libId, "shivavariantcalling", "files", "pipeline", variantCaller, "md5")}</td>
</tr>
#end
</tbody>
</table>
</div>
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