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biopet.biopet
Commit 763f8f4d authored by Vorderman's avatar Vorderman
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Gearsreport completely defutured

parent 97661f8f
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Showing with 223 additions and 165 deletions
flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala
View file @ 763f8f4d
...@@ -16,20 +16,22 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep ...@@ -16,20 +16,22 @@ package nl.lumc.sasc.biopet.pipelines.flexiprep
import java.io.{File, PrintWriter} import java.io.{File, PrintWriter}
import nl.lumc.sasc.biopet.core.report.{
ReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.core.report.{ReportBuilder, ReportBuilderExtension, ReportPage, ReportSection}
import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport.runId
import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot import nl.lumc.sasc.biopet.utils.rscript.StackedBarPlot
import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Sample}
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.Schema.Sample
import nl.lumc.sasc.biopet.utils.summary.db.Schema.Library
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._ import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._
import scala.collection.mutable import scala.collection.mutable.ArrayBuffer
import scala.collection.mutable.{ArrayBuffer, ListBuffer}
import scala.concurrent.{Await, Future}
import scala.concurrent.duration.Duration import scala.concurrent.duration.Duration
import scala.concurrent.{Await, Future}
class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension { class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension {
def builder = FlexiprepReport def builder = FlexiprepReport
...@@ -84,30 +86,31 @@ object FlexiprepReport extends ReportBuilder { ...@@ -84,30 +86,31 @@ object FlexiprepReport extends ReportBuilder {
name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp", name -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFastQcPlot.ssp",
Map("plot" -> tag)) Map("plot" -> tag))
} }
/**
* Generates the lines for readSummaryPlot /**
* @param read Must give "R1" or "R2" * Generates the lines for readSummaryPlot
* @param summary Summary class * @param read Must give "R1" or "R2"
* @param sampleId Default selects all samples, when given plot is limits on given sample * @param summary Summary class
*/ * @param sampleId Default selects all samples, when given plot is limits on given sample
def readSummaryPlotLines(read: String, */
summary: SummaryDb, def readSummaryPlotLines(read: String,
sampleId: Option[Int] = None) : Seq[String] = { summary: SummaryDb,
sampleId: Option[Int] = None): Seq[String] = {
val seqstatPaths = Map("num_total" -> List("reads", "num_total")) val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val seqstatStats = val seqstatStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = seqstatPaths) summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = seqstatPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, val seqstatQcStats = summary.getStatsForLibraries(runId,
"flexiprep", "flexiprep",
"seqstat_" + read + "_qc", "seqstat_" + read + "_qc",
keyValues = seqstatPaths) keyValues = seqstatPaths)
val clippingPaths = Map( val clippingPaths = Map(
"num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"), "num_reads_discarded_too_short" -> List("num_reads_discarded_too_short"),
"num_reads_discarded_too_long" -> List("num_reads_discarded_too_long")) "num_reads_discarded_too_long" -> List("num_reads_discarded_too_long"))
val clippingStats = summary.getStatsForLibraries(runId, val clippingStats = summary.getStatsForLibraries(runId,
"flexiprep", "flexiprep",
"clipping_" + read, "clipping_" + read,
keyValues = clippingPaths) keyValues = clippingPaths)
val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read)) val trimmingPaths = Map("num_reads_discarded" -> List("num_reads_discarded_" + read))
val trimmingStats = val trimmingStats =
...@@ -155,8 +158,7 @@ def readSummaryPlotLines(read: String, ...@@ -155,8 +158,7 @@ def readSummaryPlotLines(read: String,
def readSummaryPlot(outputDir: File, def readSummaryPlot(outputDir: File,
prefix: String, prefix: String,
read: String, read: String,
summaryPlotLines: Seq[String]) summaryPlotLines: Seq[String]): Unit = {
: Unit = {
val tsvFile = new File(outputDir, prefix + ".tsv") val tsvFile = new File(outputDir, prefix + ".tsv")
val pngFile = new File(outputDir, prefix + ".png") val pngFile = new File(outputDir, prefix + ".png")
val tsvWriter = new PrintWriter(tsvFile) val tsvWriter = new PrintWriter(tsvFile)
...@@ -181,19 +183,17 @@ def readSummaryPlotLines(read: String, ...@@ -181,19 +183,17 @@ def readSummaryPlotLines(read: String,
* @param summary Summary class * @param summary Summary class
* @param sampleId Default selects all samples, when given plot is limits on given sample * @param sampleId Default selects all samples, when given plot is limits on given sample
*/ */
def baseSummaryPlotLines(read: String,
summary: SummaryDb,
def baseSummaryPlotLines (read: String, sampleId: Option[Int] = None): Seq[String] = {
summary: SummaryDb,
sampleId: Option[Int] = None): Seq[String] = {
val statsPaths = Map("num_total" -> List("bases", "num_total")) val statsPaths = Map("num_total" -> List("bases", "num_total"))
val seqstatStats = val seqstatStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = statsPaths) summary.getStatsForLibraries(runId, "flexiprep", "seqstat_" + read, keyValues = statsPaths)
val seqstatQcStats = summary.getStatsForLibraries(runId, val seqstatQcStats = summary.getStatsForLibraries(runId,
"flexiprep", "flexiprep",
"seqstat_" + read + "_qc", "seqstat_" + read + "_qc",
keyValues = statsPaths) keyValues = statsPaths)
val libraries = val libraries =
Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf) Await.result(summary.getLibraries(runId = runId, sampleId = sampleId), Duration.Inf)
...@@ -215,7 +215,7 @@ def readSummaryPlotLines(read: String, ...@@ -215,7 +215,7 @@ def readSummaryPlotLines(read: String,
summaryPlotLines += sb.toString summaryPlotLines += sb.toString
} }
summaryPlotLines summaryPlotLines
} }
/** /**
...@@ -224,7 +224,7 @@ def readSummaryPlotLines(read: String, ...@@ -224,7 +224,7 @@ def readSummaryPlotLines(read: String,
* @param prefix prefix for tsv and png file * @param prefix prefix for tsv and png file
* @param read Must give "R1" or "R2" * @param read Must give "R1" or "R2"
* @param summaryPlotLines A sequence of strings written to the summary tsv * @param summaryPlotLines A sequence of strings written to the summary tsv
*/ */
def baseSummaryPlot(outputDir: File, def baseSummaryPlot(outputDir: File,
prefix: String, prefix: String,
read: String, read: String,
...@@ -234,7 +234,7 @@ def readSummaryPlotLines(read: String, ...@@ -234,7 +234,7 @@ def readSummaryPlotLines(read: String,
val tsvWriter = new PrintWriter(tsvFile) val tsvWriter = new PrintWriter(tsvFile)
tsvWriter.println("Library\tAfter_QC\tDiscarded") tsvWriter.println("Library\tAfter_QC\tDiscarded")
for (line <- summaryPlotLines){ for (line <- summaryPlotLines) {
tsvWriter.println(line) tsvWriter.println(line)
} }
...@@ -288,8 +288,11 @@ object FlexiprepReadSummary { ...@@ -288,8 +288,11 @@ object FlexiprepReadSummary {
val clipCount = settings.count(_._2.getOrElse("skip_clip", None).contains(false)) val clipCount = settings.count(_._2.getOrElse("skip_clip", None).contains(false))
val librariesCount = libraries.size val librariesCount = libraries.size
val summaryPlotLinesR1 = if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId) val summaryPlotLinesR1 =
val summaryPlotlinesR2 = if (showPlot && paired) FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId) if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 =
if (showPlot && paired)
FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val seqstatPaths = Map("num_total" -> List("reads", "num_total")) val seqstatPaths = Map("num_total" -> List("reads", "num_total"))
val clippingPaths = Map( val clippingPaths = Map(
...@@ -306,7 +309,6 @@ object FlexiprepReadSummary { ...@@ -306,7 +309,6 @@ object FlexiprepReadSummary {
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1", sampleId, trimmingPaths) summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1", sampleId, trimmingPaths)
Map( Map(
"summary" -> summary,
"runId" -> runId, "runId" -> runId,
"sampleId" -> sampleId, "sampleId" -> sampleId,
"libId" -> libId, "libId" -> libId,
...@@ -337,24 +339,38 @@ object FlexiprepBaseSummary { ...@@ -337,24 +339,38 @@ object FlexiprepBaseSummary {
showPlot: Boolean = false, showPlot: Boolean = false,
showTable: Boolean = true, showTable: Boolean = true,
showIntro: Boolean = true, showIntro: Boolean = true,
multisample: Boolean = true): Map[String,Any] = { multisample: Boolean = true): Map[String, Any] = {
val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples) val samples = sampleId.map(id => allSamples.filter(_.id == id)).getOrElse(allSamples)
val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries) val libraries = libId.map(id => allLibraries.filter(_.id == id)).getOrElse(allLibraries)
val librariesCount = libraries.size val librariesCount = libraries.size
val settings = summary.getSettingsForLibraries(runId, "flexiprep", keyValues = Map( val settings = summary.getSettingsForLibraries(runId,
"skip_trim" -> List("skip_trim"), "skip_clip" -> List("skip_clip"), "paired" -> List("paired"))) "flexiprep",
keyValues =
Map("skip_trim" -> List("skip_trim"),
"skip_clip" -> List("skip_clip"),
"paired" -> List("paired")))
settings.count(_._2.getOrElse("skip_trim", None) == Some(true)) settings.count(_._2.getOrElse("skip_trim", None) == Some(true))
val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false)) val trimCount = settings.count(_._2.getOrElse("skip_trim", None) == Some(false))
val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false)) val clipCount = settings.count(_._2.getOrElse("skip_clip", None) == Some(false))
val paired: Boolean = if (sampleId.isDefined && libId.isDefined) val paired: Boolean =
summary.getSettingKeys(runId, "flexiprep", NoModule, SampleId(sampleId.get), LibraryId(libId.get), keyValues = Map("paired" -> List("paired"))).getOrElse("paired", None) == Some(true) if (sampleId.isDefined && libId.isDefined)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1 summary
.getSettingKeys(runId,
"flexiprep",
NoModule,
SampleId(sampleId.get),
LibraryId(libId.get),
keyValues = Map("paired" -> List("paired")))
.getOrElse("paired", None) == Some(true)
else settings.count(_._2.getOrElse("paired", None) == Some(true)) >= 1
val summaryPlotLinesR1 = if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId) val summaryPlotLinesR1 =
val summaryPlotlinesR2 = if (showPlot && paired) FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId) if (showPlot) FlexiprepReport.readSummaryPlotLines("R1", summary, sampleId = sampleId)
val summaryPlotlinesR2 =
if (showPlot && paired)
FlexiprepReport.readSummaryPlotLines("R2", summary, sampleId = sampleId)
val statsPaths = Map("num_total" -> List("bases", "num_total")) val statsPaths = Map("num_total" -> List("bases", "num_total"))
...@@ -363,14 +379,21 @@ object FlexiprepBaseSummary { ...@@ -363,14 +379,21 @@ object FlexiprepBaseSummary {
val seqstatQCStats = val seqstatQCStats =
summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1_QC", sampleId, statsPaths) summary.getStatsForLibraries(runId, "flexiprep", "seqstat_R1_QC", sampleId, statsPaths)
Map( Map(
"trimCount" -> trimCount, "runId" -> runId,
"librariesCount" -> librariesCount, "sampleId" -> sampleId,
"clipCount" -> clipCount, "libId" -> libId,
"paired" -> paired, "showPlot" -> showPlot,
"summaryPlotLinesR1" -> summaryPlotLinesR1, "settings" -> settings,
"summaryPlotLinesR2" -> summaryPlotlinesR2 "samples" -> samples,
"libraries" -> libraries,
"trimCount" -> trimCount,
"clipCount" -> clipCount,
"librariesCount" -> librariesCount,
"seqstatStats" -> seqstatStats,
"seqstatQCStats" -> seqstatQCStats,
"summaryPlotLinesR1" -> summaryPlotLinesR1,
"summaryPlotLinesR2" -> summaryPlotlinesR2
) )
} }
} }
\ No newline at end of file
gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala
View file @ 763f8f4d
...@@ -16,8 +16,17 @@ package nl.lumc.sasc.biopet.pipelines.gears ...@@ -16,8 +16,17 @@ package nl.lumc.sasc.biopet.pipelines.gears
import java.io.File import java.io.File
import nl.lumc.sasc.biopet.core.report.{MultisampleReportBuilder, ReportBuilderExtension, ReportPage, ReportSection} import nl.lumc.sasc.biopet.core.report.{
import nl.lumc.sasc.biopet.pipelines.flexiprep.{FlexiprepReadSummary, FlexiprepReport} MultisampleReportBuilder,
ReportBuilderExtension,
ReportPage,
ReportSection
}
import nl.lumc.sasc.biopet.pipelines.flexiprep.{
FlexiprepBaseSummary,
FlexiprepReadSummary,
FlexiprepReport
}
import nl.lumc.sasc.biopet.pipelines.gears import nl.lumc.sasc.biopet.pipelines.gears
import nl.lumc.sasc.biopet.utils.config.Configurable import nl.lumc.sasc.biopet.utils.config.Configurable
import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb
...@@ -67,54 +76,57 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -67,54 +76,57 @@ object GearsReport extends MultisampleReportBuilder {
mustHaveSample = true) >= samples.size mustHaveSample = true) >= samples.size
val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table") val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table")
val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table") val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table")
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugePageUniqueMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_unique_report",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val centrifugePage = val centrifugePage =
if (centrifugeExecuted) if (centrifugeExecuted)
Some( Some(
"Centrifuge analysis" -> Future.successful(ReportPage( "Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> List(
Future.successful(ReportPage( "Non-unique" ->
List(), Future.successful(
List("All mappings" -> ReportSection( ReportPage(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", List(),
GearsKronaPlot.values(summary, List("All mappings" -> ReportSection(
runId, "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
"centrifuge_report", centrifugePageAllMappingsKronaPlot)),
"centrifuge_report", Map()
samples, ))),
libraries,
sampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List("Unique mappings" -> ReportSection( List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))), centrifugePageUniqueMappingsKronaPlot)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")) Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
))) )))
else None else None
val krakenPageKronaPlot = GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)
val krakenPage = val krakenPage =
if (krakenExecuted) if (krakenExecuted)
Some( Some(
"Kraken analysis" -> Future.successful(ReportPage( "Kraken analysis" -> Future.successful(
List(), ReportPage(
List( List(),
"Krona plot" -> Future.successful( List("Krona plot" -> Future.successful(
ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
GearsKronaPlot krakenPageKronaPlot))),
.values(summary, Map()
runId, )))
"Krona",
"krakenkrona",
samples,
libraries,
sampleId,
libId)))),
Map()
)))
else None else None
val qiimeClosedPage = val qiimeClosedPage =
...@@ -141,7 +153,10 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -141,7 +153,10 @@ object GearsReport extends MultisampleReportBuilder {
))) )))
else None else None
val flexiprepReadSummary = FlexiprepReadSummary.values(summary,runId,samples,libraries,sampleId,libId, true, false) val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId, libId, true, false)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId, libId, true, false)
Future { Future {
ReportPage( ReportPage(
List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List( List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List(
...@@ -154,7 +169,7 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -154,7 +169,7 @@ object GearsReport extends MultisampleReportBuilder {
flexiprepReadSummary), flexiprepReadSummary),
"QC bases" -> ReportSection( "QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp", "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
Map("showPlot" -> true, "showTable" -> false)) flexiprepBaseSummary)
), ),
pageArgs pageArgs
) )
...@@ -186,51 +201,55 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -186,51 +201,55 @@ object GearsReport extends MultisampleReportBuilder {
val qiimeOpenOtuTable = Await.result( val qiimeOpenOtuTable = Await.result(
summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"), summary.getFile(runId, "gearssingle", NoModule, sampleId, NoLibrary, "qiime_open_otu_table"),
Duration.Inf) Duration.Inf)
val centrifugePageAllMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_report",
"centrifuge_report",
samples,
libraries,
sampleId,
libId,
Some("centrifuge"))
val centrifugePageUniqueMappingsKronaPlot = GearsKronaPlot.values(summary,
runId,
"centrifuge_unique_report",
"centrifuge_unique_report",
samples,
libraries,
sampleId,
libId)
val gearsCentrifugePage = if (centrifugeExecuted) { val gearsCentrifugePage = if (centrifugeExecuted) {
Some( Some(
"Centrifuge analysis" -> Future.successful(ReportPage( "Centrifuge analysis" -> Future.successful(ReportPage(
List("Non-unique" -> Future.successful(ReportPage( List(
List(), "Non-unique" -> Future.successful(
List("All mappings" -> ReportSection( ReportPage(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", List(),
GearsKronaPlot.values(summary, List("All mappings" -> ReportSection(
runId, "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
"centrifuge_report", centrifugePageAllMappingsKronaPlot
"centrifuge_report", )),
samples, Map()
libraries, ))),
sampleId,
libId,
Some("centrifuge"))
)),
Map()
))),
List("Unique mappings" -> ReportSection( List("Unique mappings" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
Map("summaryStatsTag" -> "centrifuge_unique_report"))), centrifugePageUniqueMappingsKronaPlot)),
Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge")) Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))
))) )))
} else None } else None
val krakenPageKronaPlot = GearsKronaPlot
.values(summary, runId, "Krona", "krakenkrona", samples, libraries, sampleId, libId)
val krakenAnalysisPage = val krakenAnalysisPage =
if (krakenExecuted) if (krakenExecuted)
Some( Some(
"Kraken analysis" -> Future.successful(ReportPage( "Kraken analysis" -> Future.successful(
List(), ReportPage(
List( List(),
"Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", List("Krona plot" -> ReportSection(
GearsKronaPlot "/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp",
.values(summary, krakenPageKronaPlot)),
runId, Map()
"Krona", )))
"krakenkrona",
samples,
libraries,
sampleId,
libId))),
Map()
)))
else None else None
val qiimeClosesOtuTablePage = val qiimeClosesOtuTablePage =
...@@ -257,6 +276,10 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -257,6 +276,10 @@ object GearsReport extends MultisampleReportBuilder {
))) )))
else None else None
val flexiprepReadSummary =
FlexiprepReadSummary.values(summary, runId, samples, libraries, sampleId)
val flexiprepBaseSummary =
FlexiprepBaseSummary.values(summary, runId, samples, libraries, sampleId)
Future { Future {
ReportPage( ReportPage(
subPages = subPages =
...@@ -268,9 +291,11 @@ object GearsReport extends MultisampleReportBuilder { ...@@ -268,9 +291,11 @@ object GearsReport extends MultisampleReportBuilder {
), ),
sections = List( sections = List(
"QC reads" -> ReportSection( "QC reads" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp"), "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepReadSummary.ssp",
flexiprepReadSummary),
"QC bases" -> ReportSection( "QC bases" -> ReportSection(
"/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp") "/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepBaseSummary.ssp",
flexiprepBaseSummary)
),