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biopet.biopet
Commit 9817ac95 authored by Peter van 't Hof's avatar Peter van 't Hof
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Fixing some templates

parent eb4539c3
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Showing with 159 additions and 193 deletions
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ 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)
<br/>
......@@ -69,12 +67,12 @@
<th>(%)</th>
</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).sorted
case _ => summary.libraries(sample).toList.sorted
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/${sample}/index.html">${sample}</a></td>
......@@ -82,11 +80,17 @@
#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 total = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "All")):_*).getOrElse(0L).asInstanceOf[Long]
val mapped = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Mapped")):_*).getOrElse(0L).asInstanceOf[Long]
val duplicates = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "Duplicates")):_*).getOrElse(0L).asInstanceOf[Long]
val secondary = summary.getValue((prefixPath ::: List("bamstats", "flagstats", "NotPrimaryAlignment")):_*).getOrElse(0L).asInstanceOf[Long]
val statsPaths = Map(
"All" -> List("flagstats", "All"),
"Mapped" -> List("flagstats", "Mapped"),
"Duplicates" -> List("flagstats", "Duplicates"),
"NotPrimaryAlignment" -> List("flagstats", "NotPrimaryAlignment")
)
val results = summary.getStatKeys(runId, Right("bammetrics"), Some(Right("bamstats")), sample = Some(Left(sample.id)), library = libId.map(Left(_)), keyValues = statsPaths)
val total = results("All").getOrElse(0L).asInstanceOf[Long]
val mapped = results("Mapped").getOrElse(0L).asInstanceOf[Long]
val duplicates = results("Duplicates").getOrElse(0L).asInstanceOf[Long]
val secondary = results("NotPrimaryAlignment").getOrElse(0L).asInstanceOf[Long]
}#
<td>${total}</td>
<td>${mapped}</td>
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/clipping.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
#{
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)
......@@ -42,7 +38,7 @@
#end
#if (showPlot)
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.clippingPlot(outputDir, "clipping", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="clipping.png" class="img-responsive" />
......@@ -71,12 +67,12 @@
#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/${sample}/index.html">${sample}</a></td>
......@@ -84,14 +80,11 @@
#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("bamstats", "clipping", "general", field)):_*).getOrElse("N/A")
}
val statsPaths = fields.map(x => x -> List("clipping", "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 (value <- fieldValues)
<td>${value}</td>
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
#end
......
bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/mappingQuality.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 rootPath: String %>
<%@ var metricsTag: String = "bammetrics" %>
<%@ var summary: SummaryDb %>
<%@ var sampleId: Option[Int] = None %>
<%@ var libId: Option[Int] = None %>
<%@ var sampleLevel: Boolean = false %>
<%@ var rootPath: String %>
<%@ var outputDir: File %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
<%@ var showPlot: Boolean = false %>
<%@ var showTable: Boolean = true %>
<%@ var showIntro: Boolean = true%>
<%@ var runId: Int %>
<%@ var fields: List[String] = List("min", "max", "mean", "median", "modal")%>
#{
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)
......@@ -42,7 +39,7 @@
#end
#if (showPlot)
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
#{ BammetricsReport.mappingQualityPlot(outputDir, "mapping_quality", summary, !sampleLevel, sampleId = sampleId, libraryId = libId) }#
<div class="panel-body">
<img src="mapping_quality.png" class="img-responsive" />
......@@ -71,12 +68,12 @@
#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/${sample}/index.html">${sample}</a></td>
......@@ -84,14 +81,11 @@
#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("bamstats", "mapping_quality", "general", field)):_*).getOrElse("N/A")
}
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 (value <- fieldValues)
<td>${value}</td>
#for (field <- fields)
<td>${results(field)}</td>
#end
</tr>
#end
......
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/executables.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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] = None %>
<%@ var libId: Option[String] = None %>
<%@ var pipeline: String = summary.getValue("meta", "pipeline_name").getOrElse("").toString %>
<%@ var runId: Int %>
#{
val executables = summary.getValue(sampleId, libId, pipeline, "executables").getOrElse(Map()).asInstanceOf[Map[String, Map[String, Any]]]
val executables = Await.result(summary.getExecutables(runId = Some(runId)), Duration.Inf)
}#
<table class="table">
......@@ -17,11 +17,11 @@
</tr>
</thead>
<tbody>
#for (name <- executables.keySet.toList.sorted)
#for (exe <- executables.sortBy(_.toolName))
<tr>
<td>${name}</td>
<td>${exe.toolName}</td>
#{
val version = executables(name).get("version") match {
val version = exe.version match {
case Some(x) if x != None => x.toString
case _ => "N/A"
}
......
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/librariesList.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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] = None %>
<%@ var sampleId: Option[Int] = None %>
<%@ var runId: Int %>
<table class="table">
<thead><tr><th>Libraries</th></tr></thead>
<tbody>
#for (lib <- summary.libraries(sampleId.get).toList.sorted)
<tr><td><a href="${rootPath}Samples/${sampleId}/Libraries/${lib}/index.html">${lib}</a></td></tr>
#for (lib <- Await.result(summary.getLibraries(runId = Some(runId)), Duration.Inf))
<tr><td><a href="${rootPath}Samples/${Await.result(summary.getSampleName(lib.sampleId), Duration.Inf)}/Libraries/${lib.name}/index.html">${lib}</a></td></tr>
#end
</tbody>
</table>
\ No newline at end of file
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/main.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
<%@ var summary: SummaryDb %>
<%@ var indexPage: ReportPage %>
<%@ var reportName: String %>
<%@ var page: ReportPage %>
......
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/reference.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 pipeline: String %>
<%@ var runId: Int %>
#{
val contigs = summary.getValue(pipeline, "settings", "reference", "contigs").getOrElse(Map.empty).asInstanceOf[Map[String, Map[String, Any]]]
val settings = summary.getSettingKeys(runId, Right(pipeline),
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
"name" -> List("reference", "name")
))
val contigs = settings.getOrElse("contigs", Some(Map.empty)).get.asInstanceOf[Map[String, Map[String, Any]]]
val referenceFile = Await.result(summary.getFile(runId, pipeline, None, None, None, key = "referenceFasta"), Duration.Inf)
}#
<table class="table">
<tbody>
<tr><th>Species</th><td>${summary.getValue(pipeline, "settings", "reference", "species")}</td></tr>
<tr><th>Name</th><td>${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>File</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "path")}</td></tr>
<tr><th>MD5</th><td>${summary.getValue(pipeline, "files", "pipeline", "referenceFasta", "md5")}</td></tr>
<tr><th>Species</th><td>${settings.get("species")}</td></tr>
<tr><th>Name</th><td>${settings.get("name")}</td></tr>
<tr><th>File</th><td>${referenceFile.map(_.path)}</td></tr>
<tr><th>MD5</th><td>${referenceFile.map(_.md5)}</td></tr>
</tbody>
</table>
......
biopet-core/src/main/resources/nl/lumc/sasc/biopet/core/report/samplesList.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 runId: Int %>
<table class="table sortable-theme-bootstrap" data-sortable>
<thead><tr><th data-sorted="true" data-sorted-direction="ascending">Sample</th></tr></thead>
<tbody>
#for (sample <- summary.samples.toList.sorted)
<tr><td><a href="${rootPath}Samples/${sample}/index.html">${sample}</a></td></tr>
#for (sample <- Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf))
<tr><td><a href="${rootPath}Samples/${sample.name}/index.html">${sample.name}</a></td></tr>
#end
</tbody>
</table>
\ No newline at end of file
biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala
View file @ 9817ac95
......@@ -407,9 +407,9 @@ class SummaryDb(val db: Database) extends Closeable {
}
def getFile(runId: Int, pipelineName: String, moduleName: Option[String], sampleName: Option[String],
libraryName: Option[String], key: String): Future[Option[File]] = {
libraryName: Option[String], key: String): Future[Option[Schema.File]] = {
db.run(filesFilter(runId = Some(runId), pipelineName = Some(pipelineName), moduleName = Some(moduleName),
sampleName = Some(sampleName), libraryName = Some(libraryName), key = Some(key)).map(_.path).result).map(_.headOption.map(new File(_)))
sampleName = Some(sampleName), libraryName = Some(libraryName), key = Some(key)).result).map(_.headOption)
}
/** Creates a file. This method will raise expection if it already exist */
......
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/mappingFront.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#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 pipeline: String %>
<%@ var runId: Int %>
<%@ var sampleId: Option[Int] %>
<%@ var libId: Option[Int] %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
val settings = summary.getSettingKeys(runId, Right(pipeline),
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
"name" -> List("reference", "name")
))
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>Mapping</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_hash")}</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>${libId}</td></tr>
<tr><th>Pipeline</th><td>${pipeline}</td></tr>
<tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${run.outputDir}</td></tr>
<tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
<tr><th>Sample</th><td>${sampleId}</td></tr>
<tr><th>Library</th><td>${libId}</td></tr>
</tbody>
</table>
<br/>
......
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
View file @ 9817ac95
#import(nl.lumc.sasc.biopet.utils.summary.Summary)
#import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb)
#import(nl.lumc.sasc.biopet.core.report.ReportPage)
<%@ var summary: Summary %>
#import(scala.concurrent.Await)
#import(scala.concurrent.duration.Duration)
<%@ var summary: SummaryDb %>
<%@ var rootPath: String %>
<%@ var pipeline: String %>
<%@ var runId: Int %>
#{
val run = Await.result(summary.getRuns(runId = Some(runId)), Duration.Inf).head
val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf)
val settings = summary.getSettingKeys(runId, Right(pipeline),
keyValues = Map(
"contigs" -> List("reference", "contigs"),
"species" -> List("reference", "species"),
"name" -> List("reference", "name")
))
}#
<table class="table">
<tbody>
<tr><th>Pipeline</th><td>${pipeline}</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_hash")}</td></tr>
<tr><th>Output directory</th><td>${summary.getValue("meta", "output_dir")}</td></tr>
<tr><th>Reference</th><td>${summary.getValue(pipeline, "settings", "reference", "species")} - ${summary.getValue(pipeline, "settings", "reference", "name")}</td></tr>
<tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
<tr><th>Version</th><td>${run.version}</td></tr>
<tr><th>Last commit hash</th><td>${run.commitHash}</td></tr>
<tr><th>Output directory</th><td>${run.outputDir}</td></tr>
<tr><th>Reference</th><td>${settings.get("species")} - ${settings.get("name")}</td></tr>
<tr><th>Number of samples</th><td>${samples.size}</td></tr>
</tbody>
</table>
<br/>
......
mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp deleted 100644 → 0
View file @ eb4539c3
#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 %>
<%@ var pipelineName: String = "mapping" %>
<%@ var fileTag: String = "output_bamfile" %>
#{
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
}
}
}#
<div class="panel-body">
<!-- Table -->
<table class="table">
<thead><tr>
<th>Sample</th>
#if (!sampleLevel) <th>Library</th> #end
<th>Path</th>
<th>MD5</th>
</tr></thead>
<tbody>
#for (sample <- samples.toList.sorted)
#{
val libs = (libId, sampleLevel) match {
case (_, true) => List("")
case (Some(libId), _) => List(libId.toString).sorted
case _ => summary.libraries(sample).toList.sorted
}
}#
<tr><td rowspan="${libs.size}"><a href="${rootPath}Samples/${sample}/index.html">${sample}</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
<td>${removeDir(summary.getValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "path"))}</td>
<td>${summary.getValue(Some(sample), (if (sampleLevel) None else Some(libId)), pipelineName, "files", "pipeline", fileTag, "md5")}</td>
</tr>
#end
#end
</tbody>
</table>
</div>
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala
View file @ 9817ac95
......@@ -55,11 +55,7 @@ object MappingReport extends ReportBuilder {
bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List(
"Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
)), Map()),
"Files" -> ReportPage(List(), (if (skipFlexiprep) Nil else 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"))) :::
List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false))
), Map())
"Files" -> ReportPage(List(), Nil, Map())
) :::
(if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
"Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
......
mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
View file @ 9817ac95
......@@ -115,13 +115,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
def filesPage: ReportPage = {
val flexiprepExecuted = Await.result(summary.getStatsSize(runId, Right("flexiprep"), Some(None), mustHaveLibrary = true), Duration.Inf) >= 1
ReportPage(List(), (if (flexiprepExecuted) 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"))
else Nil) :::
List("Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
Map("pipelineName" -> pipelineName, "fileTag" -> "output_bam_preprocess"))), Map())
ReportPage(List(), Nil, Map())
}
/** Single sample page */
......
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