diff --git a/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..9c055ad97492ba782453472a4d7528f92dc28ade
--- /dev/null
+++ b/public/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp
@@ -0,0 +1,93 @@
+#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)
+#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 sampleLevel: Boolean = false %>
+<%@ var outputDir: File %>
+<%@ var fields: List[String] = List("PF_ALIGNED_BASES", "MEDIAN_5PRIME_BIAS", "MEDIAN_3PRIME_BIAS", "MEDIAN_5PRIME_TO_3PRIME_BIAS")%>
+<%@ var showPlot: Boolean = false %>
+<%@ var showTable: Boolean = true %>
+<%@ var showIntro: Boolean = true%>
+#{
+ val samples = sampleId match {
+ case Some(sample) => {
+ List(sample.toString)
+ }
+ case _ => summary.samples.toList
+ }
+}#
+
+#if (showIntro)
+ <br/>
+ <div class="row">
+ <div class="col-md-1"></div>
+ <div class="col-md-6">
+ <p>
+ This Show the relative coverage for all transcripts. De data here is generated by picard CollectRnaMetrics
+ </p>
+ </div>
+ </div>
+#end
+
+#if (showPlot)
+ #{ BammetricsReport.rnaHistogramPlot(outputDir, "rna", summary, !sampleLevel, sampleId = sampleId, libId = libId) }#
+
+ <div class="panel-body">
+ <img src="rna.png" class="img-responsive" />
+ </div>
+ <div class="panel-footer">
+ #if (showTable)
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Hide table</button>
+ #else
+ <button type="button" class="btn btn-info" data-toggle="collapse" data-target="#rnaTable">Show table</button>
+ #end
+ <i class="glyphicon glyphicon-file"></i> <a href="rna.tsv">tsv file</a>
+ </div>
+#end
+
+<div class="panel-body collapse #if (showTable)in#end" id="rnaTable">
+<!-- Table -->
+<table class="table sortable-theme-bootstrap" data-sortable>
+ <thead><tr>
+ <th data-sorted="true" data-sorted-direction="ascending">Sample</th>
+ #if (!sampleLevel) <th>Library</th> #end
+ #for (field <- fields)
+ <th>${field.replaceAll("_", " ")}</th>
+ #end
+ </tr></thead>
+ <tbody>
+ #for (sample <- samples.toList.sorted)
+ #{
+ val libs = (libId, sampleLevel) match {
+ case (_, true) => List("")
+ case (Some(libId), _) => List(libId.toString)
+ case _ => summary.libraries(sample).toList
+ }
+ }#
+ <tr><td rowspan="${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">${libId}</a></td> #end
+ #{
+ val prefixPath = List("samples", sample) ::: (if (libId.isEmpty) Nil else List("libraries", libId)) ::: List("bammetrics", "stats")
+
+ val fieldValues = for (field <- fields) yield {
+ summary.getValue((prefixPath ::: List("rna", "metrics", field.toUpperCase)):_*).getOrElse(prefixPath ::: metricsTag :: Nil)
+ }
+ }#
+ #for (value <- fieldValues)
+ <td>${value}</td>
+ #end
+ </tr>
+ #end
+ #end
+ </tbody>
+</table>
+
+</div>
diff --git a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
index 4da9ec9e5f878262e66473d559cc209580674992..10cecfb2d8c54ff18c78fc74385993bcf17312d7 100644
--- a/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
+++ b/public/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala
@@ -57,9 +57,13 @@ object BammetricsReport extends ReportBuilder {
sampleId: Option[String],
libId: Option[String],
metricsTag: String = "bammetrics") = {
+
+ val wgsExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "wgs").isDefined
+ val rnaExecuted = summary.getValue(sampleId, libId, metricsTag, "stats", "rna").isDefined
+
val targets = (
- summary.getValue(sampleId, libId, "bammetrics", "settings", "amplicon_name"),
- summary.getValue(sampleId, libId, "bammetrics", "settings", "roi_name")
+ summary.getValue(sampleId, libId, metricsTag, "settings", "amplicon_name"),
+ summary.getValue(sampleId, libId, metricsTag, "settings", "roi_name")
) match {
case (Some(amplicon: String), Some(roi: List[_])) => amplicon :: roi.map(_.toString)
case (_, Some(roi: List[_])) => roi.map(_.toString)
@@ -74,9 +78,13 @@ object BammetricsReport extends ReportBuilder {
Map())),
List(
"Summary" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
- "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true)),
- "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp", Map("showPlot" -> true))
- ),
+ "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp", Map("showPlot" -> true))
+ ) ++ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+ Map("showPlot" -> true)))
+ else Nil) ++
+ (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+ Map("showPlot" -> true)))
+ else Nil),
Map("metricsTag" -> metricsTag)
)
}
@@ -321,4 +329,94 @@ object BammetricsReport extends ReportBuilder {
plot.title = Some("Whole genome coverage")
plot.runLocal()
}
+
+ /**
+ * Generate a line plot for rna coverage
+ * @param outputDir OutputDir for the tsv and png file
+ * @param prefix Prefix of the tsv and png file
+ * @param summary Summary class
+ * @param libraryLevel Default false, when set true plot will be based on library stats instead of sample stats
+ * @param sampleId Default it selects all sampples, when sample is giving it limits to selected sample
+ */
+ def rnaHistogramPlot(outputDir: File,
+ prefix: String,
+ summary: Summary,
+ libraryLevel: Boolean = false,
+ sampleId: Option[String] = None,
+ libId: Option[String] = None): Unit = {
+ val tsvFile = new File(outputDir, prefix + ".tsv")
+ val pngFile = new File(outputDir, prefix + ".png")
+ val tsvWriter = new PrintWriter(tsvFile)
+ if (libraryLevel) {
+ tsvWriter.println((for (
+ sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+ ) yield s"$sample-$lib")
+ .mkString("library\t", "\t", ""))
+ } else {
+ sampleId match {
+ case Some(sample) => tsvWriter.println("\t" + sample)
+ case _ => tsvWriter.println(summary.samples.mkString("Sample\t", "\t", ""))
+ }
+ }
+
+ var map: Map[Int, Map[String, Double]] = Map()
+
+ def fill(sample: String, lib: Option[String]): Unit = {
+
+ val insertSize = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "normalized_position"),
+ summary, Some(sample), lib).value.getOrElse(List())
+ val counts = new SummaryValue(List("bammetrics", "stats", "rna", "histogram", "All_Reads.normalized_coverage"),
+ summary, Some(sample), lib).value.getOrElse(List())
+
+ (insertSize, counts) match {
+ case (l: List[_], l2: List[_]) =>
+ l.zip(l2).foreach(i => {
+ val insertSize = i._1.toString.toInt
+ val count = i._2.toString.toDouble
+ val old = map.getOrElse(insertSize, Map())
+ if (libraryLevel) map += insertSize -> (old + ((s"$sample-" + lib.get) -> count))
+ else map += insertSize -> (old + (sample -> count))
+ })
+ case _ => throw new IllegalStateException("Must be a list")
+ }
+ }
+
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+ ) fill(sample, Some(lib))
+ } else if (sampleId.isDefined) fill(sampleId.get, None)
+ else summary.samples.foreach(fill(_, None))
+
+ for ((insertSize, counts) <- map) {
+ tsvWriter.print(insertSize)
+ if (libraryLevel) {
+ for (
+ sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample;
+ lib <- summary.libraries(sample) if libId.isEmpty || libId.get == lib
+ ) {
+ tsvWriter.print("\t" + counts.getOrElse(s"$sample-$lib", "0"))
+ }
+ } else {
+ for (sample <- summary.samples if sampleId.isEmpty || sampleId.get == sample) {
+ tsvWriter.print("\t" + counts.getOrElse(sample, "0"))
+ }
+ }
+ tsvWriter.println()
+ }
+
+ tsvWriter.close()
+
+ val plot = new LinePlot(null)
+ plot.input = tsvFile
+ plot.output = pngFile
+ plot.xlabel = Some("Reletive position")
+ plot.ylabel = Some("Coverage")
+ plot.width = Some(1200)
+ plot.removeZero = true
+ plot.title = Some("Rna coverage")
+ plot.runLocal()
+ }
}
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
index fcc6afa62dd7ff72b046e009fdd931312214a079..17e358d2d86f870f983fe692df9c02475aabf5e4 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/Carp.scala
@@ -18,6 +18,7 @@ package nl.lumc.sasc.biopet.pipelines.carp
import java.io.File
import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.macs2.Macs2CallPeak
import nl.lumc.sasc.biopet.extensions.picard.BuildBamIndex
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
@@ -95,7 +96,7 @@ class Carp(val root: Configurable) extends QScript with MultisampleMappingTrait
}
}
- override def reportClass = {
+ override def reportClass: Option[ReportBuilderExtension] = {
val carp = new CarpReport(this)
carp.outputDir = new File(outputDir, "report")
carp.summaryFile = summaryFile
diff --git a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
index a06cef16f169732aba3ebe31357f907d24ac2eca..756d1e33d32f8008ed5c06fc0f8d2595c15d3b76 100644
--- a/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
+++ b/public/carp/src/main/scala/nl/lumc/sasc/biopet/pipelines/carp/CarpReport.scala
@@ -15,10 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.carp
+import nl.lumc.sasc.biopet.core.report.{ ReportSection, ReportBuilderExtension }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
* Class for report for CArp
@@ -29,71 +28,10 @@ class CarpReport(val root: Configurable) extends ReportBuilderExtension {
def builder = CarpReport
}
-object CarpReport extends MultisampleReportBuilder {
-
- /** Root page for the carp report */
- def indexPage = {
- //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
- ReportPage(
- List("Samples" -> generateSamplesPage(pageArgs)) ++
- Map("Files" -> filesPage,
- "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
- )), Map())
- ),
- List(
- "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"),
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
- ),
- "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
- "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false)),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false))
- ),
- pageArgs
- )
- }
-
- /** Files page, can be used general or at sample level */
- def filesPage: ReportPage = 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"),
- "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" -> "shiva", "fileTag" -> "preProcessBam"))
- ), Map())
-
- /** Single sample page */
- def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Libraries" -> generateLibraryPage(args),
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
- "Files" -> filesPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
- "Merged" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
- }
-
- /** Library page */
- def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
- "QC" -> FlexiprepReport.flexiprepPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
- }
-
+object CarpReport extends MultisampleMappingReportTrait {
/** Name of the report */
def reportName = "Carp Report"
+ override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp")
+
+ override def pipelineName = "carp"
}
\ No newline at end of file
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index fbb095945778b9dcb727cccf668f50184990e161..0eab05598fc49307439534a0845a03d415b863fd 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -19,6 +19,7 @@ import java.io.File
import nl.lumc.sasc.biopet.FullVersion
import nl.lumc.sasc.biopet.core._
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.extensions.picard.{ MergeSamFiles, SortSam }
import nl.lumc.sasc.biopet.extensions.samtools.SamtoolsView
import nl.lumc.sasc.biopet.extensions.tools.{ MergeTables, WipeReads }
@@ -53,6 +54,13 @@ class Gentrap(val root: Configurable) extends QScript
// alternative constructor for initialization with empty configuration
def this() = this(null)
+ override def reportClass: Option[ReportBuilderExtension] = {
+ val report = new GentrapReport(this)
+ report.outputDir = new File(outputDir, "report")
+ report.summaryFile = summaryFile
+ Some(report)
+ }
+
/** Split aligner to use */
var aligner: String = config("aligner", default = "gsnap")
@@ -124,8 +132,7 @@ class Gentrap(val root: Configurable) extends QScript
),
// disable markduplicates since it may not play well with all aligners (this can still be overriden via config)
"mapping" -> Map(
- "skip_markduplicates" -> true,
- "skip_metrics" -> true
+ "skip_markduplicates" -> true
)
)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
index 55f50882862db3bdc787fffdbeb6be35cf24d009..16b8a6fff7076ae9aa9d09a59c4d8fb52c4b75f9 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala
@@ -15,10 +15,9 @@
*/
package nl.lumc.sasc.biopet.pipelines.gentrap
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
import nl.lumc.sasc.biopet.utils.config.Configurable
-import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
/**
* Class to generate report for [[Gentrap]]
@@ -29,69 +28,12 @@ class GentrapReport(val root: Configurable) extends ReportBuilderExtension {
def builder = GentrapReport
}
-object GentrapReport extends MultisampleReportBuilder {
+object GentrapReport extends MultisampleMappingReportTrait {
- /** Root page for the carp report */
- def indexPage = {
- //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_))
- ReportPage(
- List("Samples" -> generateSamplesPage(pageArgs)) ++
- Map("Files" -> filesPage,
- "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
- )), Map())
- ),
- List(
- "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp"),
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
- ),
- "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false)),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false))
- ),
- pageArgs
- )
- }
-
- /** Files page, can be used general or at sample level */
- def filesPage: ReportPage = 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"),
- "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" -> "shiva", "fileTag" -> "preProcessBam"))
- ), Map())
-
- /** Single sample page */
- def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Libraries" -> generateLibraryPage(args),
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
- "Files" -> filesPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
- "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true)),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
- }
-
- /** Library page */
- def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
- "QC" -> FlexiprepReport.flexiprepPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
- }
+ override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/gentrap/gentrapFront.ssp")
/** Name of the report */
def reportName = "Gentrap Report"
+
+ override def pipelineName = "gentrap"
}
\ No newline at end of file
diff --git a/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
new file mode 100644
index 0000000000000000000000000000000000000000..a7027c4681c22f8119456fd445c5ddf83bb2366b
--- /dev/null
+++ b/public/mapping/src/main/resources/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp
@@ -0,0 +1,36 @@
+#import(nl.lumc.sasc.biopet.utils.summary.Summary)
+#import(nl.lumc.sasc.biopet.core.report.ReportPage)
+<%@ var summary: Summary %>
+<%@ var rootPath: String %>
+
+<table class="table">
+<tbody>
+ <tr><th>Pipeline</th><td>Shiva</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("shiva", "settings", "reference", "species")} - ${summary.getValue("shiva", "settings", "reference", "name")}</td></tr>
+ <tr><th>Number of samples</th><td>${summary.samples.size}</td></tr>
+</tbody>
+</table>
+<br/>
+<div class="row">
+ <div class="col-md-1"></div>
+ <div class="col-md-6">
+ <p>
+ In this web document you can find your <em>Shiva</em> pipeline report.
+ Different categories of data can be found in the left-side menu.
+ Statistics per sample and library can be accessed through the top-level menu.
+ Some statistics for target regions can be found in the regions tab.
+ Futhermore, you can view all versions of software tools used by selecting <em>Versions</em> from the top menu.
+ </p>
+
+ <p>
+ <small>Brought to you by <a href="https://sasc.lumc.nl" target="_blank"><abbr
+ title="Sequence Analysis Support Core">SASC</abbr></a> and <a
+ href="https://www.lumc.nl/org/klinische-genetica/" target="_blank"><abbr title="Clinical Genetics LUMC">KG</abbr></a>,
+ LUMC.
+ </small>
+ </p>
+ </div>
+</div>
\ No newline at end of file
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
new file mode 100644
index 0000000000000000000000000000000000000000..30e4e3e3433838cc0e07af1e54c91dca0e796b8f
--- /dev/null
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala
@@ -0,0 +1,97 @@
+package nl.lumc.sasc.biopet.pipelines.mapping
+
+import nl.lumc.sasc.biopet.core.report.{ ReportBuilderExtension, ReportSection, ReportPage, MultisampleReportBuilder }
+import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
+import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+import nl.lumc.sasc.biopet.utils.config.Configurable
+
+/**
+ * Created by pjvanthof on 11/01/16.
+ */
+class MultisampleMappingReport(val root: Configurable) extends ReportBuilderExtension {
+ def builder = MultisampleMappingReport
+}
+
+object MultisampleMappingReport extends MultisampleMappingReportTrait {
+ /** Name of the report */
+ def reportName = "Mapping Report"
+}
+
+trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
+ /** Front section for the report */
+ def frontSection: ReportSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/multisampleMappingFront.ssp")
+
+ def pipelineName = "multisamplemapping"
+
+ /** Root page for the carp report */
+ def indexPage = {
+
+ val wgsExecuted = summary.getSampleValues("bammetrics", "stats", "wgs").values.exists(_.isDefined)
+ val rnaExecuted = summary.getSampleValues("bammetrics", "stats", "rna").values.exists(_.isDefined)
+
+ ReportPage(
+ List("Samples" -> generateSamplesPage(pageArgs)) ++
+ Map("Reference" -> ReportPage(List(), List(
+ "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName))
+ ), Map()),
+ "Files" -> filesPage,
+ "Versions" -> ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"
+ )), Map())
+ ),
+ List(
+ "Report" -> frontSection,
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
+ ),
+ "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false))) ++
+ (if (wgsExecuted) List("Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
+ else Nil) ++
+ (if (rnaExecuted) List("Rna coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp",
+ Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)))
+ else Nil) ++
+ List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
+ Map("showPlot" -> true, "showTable" -> false)),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
+ Map("showPlot" -> true, "showTable" -> false))
+ ),
+ pageArgs
+ )
+ }
+
+ /** Files page, can be used general or at sample level */
+ def filesPage: ReportPage = 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"),
+ "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" -> "preProcessBam"))), Map())
+
+ /** Single sample page */
+ def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+ ReportPage(List(
+ "Libraries" -> generateLibraryPage(args),
+ "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
+ "Files" -> filesPage
+ ), List(
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
+ if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
+ "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true))) ++
+ List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+ ), args)
+ }
+
+ /** Library page */
+ def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
+ ReportPage(List(
+ "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)),
+ "QC" -> FlexiprepReport.flexiprepPage
+ ), List(
+ "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp"),
+ "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
+ "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
+ ), args)
+ }
+}
\ No newline at end of file
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
index 22066304263f234d000f2111f061e78f4ed54cb5..496ee2260d83757d8913b95e13080cc0f25080e3 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
@@ -3,6 +3,7 @@ package nl.lumc.sasc.biopet.pipelines.mapping
import java.io.File
import htsjdk.samtools.SamReaderFactory
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.core.{ PipelineCommand, Reference, MultiSampleQScript }
import nl.lumc.sasc.biopet.extensions.Ln
import nl.lumc.sasc.biopet.extensions.picard.{ MarkDuplicates, MergeSamFiles, AddOrReplaceReadGroups, SamToFastq }
@@ -37,6 +38,13 @@ trait MultisampleMappingTrait extends MultiSampleQScript
addSummaryJobs()
}
+ override def reportClass: Option[ReportBuilderExtension] = {
+ val report = new MultisampleMappingReport(this)
+ report.outputDir = new File(outputDir, "report")
+ report.summaryFile = summaryFile
+ Some(report)
+ }
+
def addMultiSampleJobs(): Unit = {
// this code will be executed after all code of all samples is executed
}
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
index 5c88189833b1b6bd169c3da475c6c2370957abf9..decc33b463fb35a03e1d6db575ae9d81cbe69fb1 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaReport.scala
@@ -17,12 +17,11 @@ package nl.lumc.sasc.biopet.pipelines.shiva
import java.io.{ File, PrintWriter }
-import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report._
-import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingReportTrait
+import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
-import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport
-import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport
+import nl.lumc.sasc.biopet.utils.summary.{ Summary, SummaryValue }
/**
* With this extension the report is executed within a pipeline
@@ -34,52 +33,32 @@ class ShivaReport(val root: Configurable) extends ReportBuilderExtension {
}
/** Object for report generation for Shiva pipeline */
-object ShivaReport extends MultisampleReportBuilder {
+object ShivaReport extends MultisampleMappingReportTrait {
def variantcallingExecuted = summary.getValue("shiva", "settings", "multisample_variantcalling") match {
case Some(true) => true
case _ => false
}
+ override def frontSection = ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")
+
+ override def pipelineName = "shiva"
+
override def extFiles = super.extFiles ++ List("js/gears.js")
.map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x))
/** Root page for the shiva report */
- def indexPage = {
+ override def indexPage = {
+ val variantcallingSection = (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
+ Map("showPlot" -> true, "showTable" -> false)))
+ else Nil)
+
val regions = regionsPage
- ReportPage(
- List("Samples" -> generateSamplesPage(pageArgs)) ++
- (if (regions.isDefined) Map(regions.get) else Map()) ++
- Map("Reference" -> ReportPage(List(), List(
- "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> "shiva"))
- ), Map()),
- "Files" -> filesPage,
- "Versions" -> ReportPage(List(), List(
- "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp")
- ), Map())
- ),
- List(
- "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/shivaFront.ssp")) ++
- (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp",
- Map("showPlot" -> true, "showTable" -> false)))
- else Nil) ++
- List("Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)
- ),
- "Insert Size" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/insertSize.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
- "Whole genome coverage" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp",
- Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false)),
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false)),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
- Map("showPlot" -> true, "showTable" -> false))
- ),
- pageArgs
- )
+ val oldPage = super.indexPage
+
+ oldPage.copy(sections = variantcallingSection ++ oldPage.sections, subPages = oldPage.subPages ++ regionsPage)
}
- //TODO: Add variants per target
/** Generate a page with all target coverage stats */
def regionsPage: Option[(String, ReportPage)] = {
val roi = summary.getValue("shiva", "settings", "regions_of_interest")
@@ -121,49 +100,19 @@ object ShivaReport extends MultisampleReportBuilder {
}
/** Files page, can be used general or at sample level */
- def filesPage: ReportPage = 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"),
- "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" -> "shiva", "fileTag" -> "preProcessBam"))) ++
- (if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
+ override def filesPage: ReportPage = {
+ val vcfFilesSection = if (variantcallingExecuted) List("VCF files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/outputVcfFiles.ssp",
Map("sampleId" -> None)))
- else Nil), Map())
-
- /** Single sample page */
- def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
- ReportPage(List(
- "Libraries" -> generateLibraryPage(args),
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), None),
- "Files" -> filesPage
- ), List(
- "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp",
- if (summary.libraries(sampleId).size > 1) Map("showPlot" -> true) else Map()),
- "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true))) ++
- (if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil) ++
- List("QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- ), args)
+ else Nil
+ val oldPage = super.filesPage
+ oldPage.copy(sections = oldPage.sections ++ vcfFilesSection)
}
- /** Library page */
- def libraryPage(sampleId: String, libId: String, args: Map[String, Any]): ReportPage = {
- val flexiprepExecuted = summary.getLibraryValue(sampleId, libId, "flexiprep").isDefined
- val krakenExecuted = summary.getValue(Some(sampleId), Some(libId), "gears", "stats", "krakenreport").isDefined
-
- ReportPage(
- "Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId)) ::
- (if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil
- ) ::: (if (krakenExecuted) List("Gears - Metagenomics" -> ReportPage(List(), List(
- "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp"
- )), Map()))
- else Nil), "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp") ::
- (if (flexiprepExecuted) List(
- "QC reads" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"),
- "QC bases" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp")
- )
- else Nil), args)
+ /** Single sample page */
+ override def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
+ val variantcallingSection = if (variantcallingExecuted) List("Variantcalling" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/shiva/sampleVariants.ssp")) else Nil
+ val oldPage = super.samplePage(sampleId, args)
+ oldPage.copy(sections = variantcallingSection ++ oldPage.sections)
}
/** Name of the report */
diff --git a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
index 58a4710cad1019ed79dba8a46a1c06053d14e436..f0fe2c1291d647815f8d336902fbd944f6312f3f 100644
--- a/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
+++ b/public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
@@ -16,8 +16,9 @@
package nl.lumc.sasc.biopet.pipelines.shiva
import nl.lumc.sasc.biopet.core.Reference
+import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension
import nl.lumc.sasc.biopet.pipelines.bammetrics.TargetRegions
-import nl.lumc.sasc.biopet.pipelines.mapping.{ MultisampleMappingTrait }
+import nl.lumc.sasc.biopet.pipelines.mapping.MultisampleMappingTrait
import nl.lumc.sasc.biopet.pipelines.toucan.Toucan
import org.broadinstitute.gatk.queue.QScript
@@ -28,7 +29,7 @@ import org.broadinstitute.gatk.queue.QScript
*/
trait ShivaTrait extends MultisampleMappingTrait with Reference with TargetRegions { qscript: QScript =>
- override def reportClass = {
+ override def reportClass: Option[ReportBuilderExtension] = {
val shiva = new ShivaReport(this)
shiva.outputDir = new File(outputDir, "report")
shiva.summaryFile = summaryFile