From 10248b225e0205a8083c26f7838ffc61284eaeef Mon Sep 17 00:00:00 2001 From: Peter van 't Hof Date: Tue, 4 Apr 2017 15:30:38 +0200 Subject: [PATCH] generelize files and version even more --- .../bammetrics/BammetricsReport.scala | 4 +- .../report/MultisampleReportBuilder.scala | 14 +++--- .../biopet/core/report/ReportBuilder.scala | 42 ++++++++++++++-- .../report/MultisampleReportBuilderTest.scala | 1 + .../core/report/ReportBuilderTest.scala | 1 + .../pipelines/flexiprep/FlexiprepReport.scala | 10 ++-- .../biopet/pipelines/gears/GearsReport.scala | 49 +++++++++++-------- .../pipelines/gears/GearsSingleReport.scala | 7 ++- .../pipelines/mapping/MappingReport.scala | 8 ++- .../mapping/MultisampleMappingReport.scala | 37 ++------------ 10 files changed, 90 insertions(+), 83 deletions(-) diff --git a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala index 4564c6de7..d4e16211b 100644 --- a/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala +++ b/bammetrics/src/main/scala/nl/lumc/sasc/biopet/pipelines/bammetrics/BammetricsReport.scala @@ -41,13 +41,15 @@ object BammetricsReport extends ReportBuilder { /** Name of report */ val reportName = "Bam Metrics" + def pipelineName = "bammetrics" + /** Root page for single BamMetrcis report */ def indexPage: Future[ReportPage] = Future { val bamMetricsPage = Await.result(this.bamMetricsPage(summary, sampleId, libId), Duration.Inf) ReportPage(bamMetricsPage.subPages ::: List( "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" )), Map())), - "Files" -> Future(ReportPage(List(), List(), Map())) + "Files" -> filesPage(sampleId, libId) ), List( "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/bamMetricsFront.ssp") ) ::: bamMetricsPage.sections, diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala index 40f8efc46..1a82b4e8d 100644 --- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala +++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilder.scala @@ -29,9 +29,7 @@ trait MultisampleReportBuilder extends ReportBuilder { /** Default list of samples, can be override */ def samplesSections: List[(String, ReportSection)] = { - List( - ("Samples", ReportSection("/nl/lumc/sasc/biopet/core/report/samplesList.ssp")) - ) + List("Samples" -> ReportSection("/nl/lumc/sasc/biopet/core/report/samplesList.ssp")) } /** Method to generate a single library page */ @@ -39,16 +37,15 @@ trait MultisampleReportBuilder extends ReportBuilder { /** Default list of libraries, can be override */ def librariesSections: List[(String, ReportSection)] = { - List( - ("Libraries", ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp")) - ) + List("Libraries" -> ReportSection("/nl/lumc/sasc/biopet/core/report/librariesList.ssp")) } /** Generate the samples page including a single sample page for each sample in the summary */ def generateSamplesPage(args: Map[String, Any]): Future[ReportPage] = Future { val samples = Await.result(summary.getSamples(runId = Some(runId)), Duration.Inf) val samplePages = samples.map(_.id) - .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId)))) + .map(sampleId => sampleId -> samplePage(sampleId, args ++ Map("sampleId" -> Some(sampleId))) + .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, None) :: Nil))) .toList ReportPage(samplePages.map(x => samples.find(_.id == x._1).get.name -> x._2), samplesSections, args) } @@ -63,7 +60,8 @@ trait MultisampleReportBuilder extends ReportBuilder { val libraries = Await.result(summary.getLibraries(runId = Some(runId), sampleId = Some(sampleId)), Duration.Inf) val libPages = libraries.map(_.id) - .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId)))) + .map(libId => libId -> libraryPage(sampleId, libId, args ++ Map("libId" -> Some(libId))) + .map(x => x.copy(subPages = x.subPages ::: "Files" -> filesPage(sampleId, libId) :: Nil))) .toList ReportPage(libPages.map(x => libraries.find(_.id == x._1).get.name -> x._2), librariesSections, args) } diff --git a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala index d34dd4614..bf79403c7 100644 --- a/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala +++ b/biopet-core/src/main/scala/nl/lumc/sasc/biopet/core/report/ReportBuilder.scala @@ -17,9 +17,10 @@ package nl.lumc.sasc.biopet.core.report import java.io._ import nl.lumc.sasc.biopet.core.ToolCommandFunction -import nl.lumc.sasc.biopet.utils.summary.db.Schema.{ Library, Module, Pipeline, Sample } +import nl.lumc.sasc.biopet.utils.summary.db.Schema.{Library, Module, Pipeline, Sample} import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb -import nl.lumc.sasc.biopet.utils.{ IoUtils, Logging, ToolCommand } +import nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.{LibraryId, SampleId} +import nl.lumc.sasc.biopet.utils.{IoUtils, Logging, ToolCommand} import org.broadinstitute.gatk.utils.commandline.Input import org.fusesource.scalate.TemplateEngine @@ -203,7 +204,7 @@ trait ReportBuilder extends ToolCommand { ) } - val rootPage = indexPage + val rootPage = indexPage.map { x => x.copy(subPages = x.subPages ::: generalPages(sampleId, libId))} // total = ReportBuilder.countPages(rootPage) logger.info(total + " pages to be generated") @@ -274,6 +275,41 @@ trait ReportBuilder extends ToolCommand { } } + + def pipelineName + + /** Files page, can be used general or at sample level */ + def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): Future[ReportPage] = { + val dbFiles = summary.getFiles(runId, sample = sampleId.map(SampleId), + library = libraryId.map(LibraryId)) + .map(_.groupBy(_.pipelineId)) + val modulePages = dbFiles.map(_.map { + case (pipelineId, files) => + val moduleSections = files.groupBy(_.moduleId).map { + case (moduleId, files) => + val moduleName: Future[String] = moduleId match { + case Some(id) => summary.getModuleName(pipelineId, id).map(_.getOrElse("Pipeline")) + case _ => Future("Pipeline") + } + moduleName.map(_ -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> files))) + } + val moduleSectionsSorted = moduleSections.find(_._1 == "Pipeline") ++ moduleSections.filter(_._1 != "Pipeline") + summary.getPipelineName(pipelineId = pipelineId).map(_.get -> Future(ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map()))) + }) + + val pipelineFiles = summary.getPipelineId(runId, pipelineName).flatMap(pipelinelineId => dbFiles.map(x => x(pipelinelineId.get).filter(_.moduleId.isEmpty))) + + modulePages.flatMap(Future.sequence(_)).map(x => ReportPage(x.toList, + s"$pipelineName files" -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> Await.result(pipelineFiles, Duration.Inf))) :: + "Sub pipelines/modules" -> ReportSection("/nl/lumc/sasc/biopet/core/report/fileModules.ssp", Map("pipelineIds" -> Await.result(dbFiles.map(_.keys.toList), Duration.Inf))) :: Nil, Map())) + } + + /** This generate general pages that all reports should have */ + def generalPages(sampleId: Option[Int], libId: Option[Int]): List[(String, Future[ReportPage])] = List( + "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp")), Map())), + "Files" -> filesPage(sampleId, libId) + ) + } object ReportBuilder { diff --git a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala index 59e6ad20a..50894f01a 100644 --- a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala +++ b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/MultisampleReportBuilderTest.scala @@ -37,6 +37,7 @@ class MultisampleReportBuilderTest extends TestNGSuite with Matchers { @Test def testGeneratePages(): Unit = { val builder = new MultisampleReportBuilder { + def pipelineName = "test" def reportName: String = "test" def indexPage: Future[ReportPage] = Future(ReportPage("Samples" -> generateSamplesPage(Map()) :: Nil, Nil, Map())) diff --git a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala index 8b8fc97c9..cbe1767d8 100644 --- a/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala +++ b/biopet-core/src/test/scala/nl/lumc/sasc/biopet/core/report/ReportBuilderTest.scala @@ -46,6 +46,7 @@ class ReportBuilderTest extends TestNGSuite with Matchers { @Test(dataProvider = "testGeneratePages") def testGeneratePages(sample: Option[String], lib: Option[String], nested: Boolean): Unit = { val builder = new ReportBuilder { + def pipelineName = "test" def reportName: String = "test" def indexPage: Future[ReportPage] = Future(ReportPage( (if (nested) "p1" -> Future(ReportPage(Nil, Nil, Map())) :: Nil else Nil), Nil, Map())) diff --git a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala index aab196af0..866f5531c 100644 --- a/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala +++ b/flexiprep/src/main/scala/nl/lumc/sasc/biopet/pipelines/flexiprep/FlexiprepReport.scala @@ -37,18 +37,14 @@ class FlexiprepReport(val parent: Configurable) extends ReportBuilderExtension { object FlexiprepReport extends ReportBuilder { val reportName = "Flexiprep" + def pipelineName = "flexiprep" + override def pageArgs = Map("multisample" -> false) /** Index page for a flexiprep report */ def indexPage: Future[ReportPage] = Future { val flexiprepPage = this.flexiprepPage - ReportPage(List("Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" - )), Map())), - "Files" -> Future(ReportPage(List(), List( //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( + ReportPage(Nil, List( "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepFront.ssp") ) ::: Await.result(flexiprepPage, Duration.Inf).sections, Map() diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala index c2b2458f2..7e6cd8e20 100644 --- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala +++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala @@ -36,6 +36,8 @@ class GearsReport(val parent: Configurable) extends ReportBuilderExtension { object GearsReport extends MultisampleReportBuilder { + def pipelineName = "gears" + def reportName = "Gears Report" override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico") @@ -49,28 +51,33 @@ object GearsReport extends MultisampleReportBuilder { val qiimeClosesOtuTable = summary.getFile(runId, "gears", key = "qiime_closed_otu_table") val qiimeOpenOtuTable = summary.getFile(runId, "gears", key = "qiime_open_otu_table") + val centrifugePage = (if (centrifugeExecuted) Some("Centriguge analysis" -> Future(ReportPage(List("Non-unique" -> + Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", + Map("summaryStatsTag" -> "centrifuge_report") + )), Map()))), List( + "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", + Map("summaryStatsTag" -> "centrifuge_unique_report") + )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))) + else None) + + val krakenPage = (if (krakenExecuted) Some("Kraken analysis" -> Future(ReportPage(List(), List( + "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" + ))), Map()))) + else None) + + val qiimeClosedPage = (if (qiimeClosesOtuTable.isDefined) Some("Qiime closed reference analysis" -> Future(ReportPage(List(), List( + "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" + ))), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeClosesOtuTable.get.path))))) + else None) + + val qiimeOpenPage = (if (qiimeOpenOtuTable.isDefined) Some("Qiime open reference analysis" -> Future(ReportPage(List(), List( + "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" + )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path))))) + else None) + ReportPage( - (if (centrifugeExecuted) List("Centriguge analysis" -> Future(ReportPage(List("Non-unique" -> - Future(ReportPage(List(), List("All mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", - Map("summaryStatsTag" -> "centrifuge_report") - )), Map()))), List( - "Unique mappings" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp", - Map("summaryStatsTag" -> "centrifuge_unique_report") - )), Map("summaryModuleTag" -> "gearscentrifuge", "centrifugeTag" -> Some("centrifuge"))))) - else Nil) ::: (if (krakenExecuted) List("Kraken analysis" -> Future(ReportPage(List(), List( - "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" - ))), Map()))) - else Nil) ::: (if (qiimeClosesOtuTable.isDefined) List("Qiime closed reference analysis" -> Future(ReportPage(List(), List( - "Krona plot" -> Future(ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" - ))), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeClosesOtuTable.get.path))))) - else Nil) ::: (if (qiimeOpenOtuTable.isDefined) List("Qiime open reference analysis" -> Future(ReportPage(List(), List( - "Krona plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/qiimeKrona.ssp" - )), Map("biomFile" -> new File(run.outputDir + File.separator + qiimeOpenOtuTable.get.path))))) - else Nil) ::: List("Samples" -> generateSamplesPage(pageArgs)) ++ - Map( - "Versions" -> Future(ReportPage(List(), List( - "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp") - ), Map())) + List(centrifugePage, krakenPage, qiimeClosedPage, qiimeOpenPage).flatten ::: List( + "Samples" -> generateSamplesPage(pageArgs) ), List( "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp")) ++ diff --git a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala index 245f521dd..edd1b0b56 100644 --- a/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala +++ b/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsSingleReport.scala @@ -28,6 +28,8 @@ class GearsSingleReport(val parent: Configurable) extends ReportBuilderExtension object GearsSingleReport extends ReportBuilder { + def pipelineName = "gearssingle" + override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico") .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x)) @@ -39,10 +41,7 @@ object GearsSingleReport extends ReportBuilder { val centrifugeExecuted = Await.result(summary.getStatsSize(runId, "gearscentrifuge", "centrifuge_report", sample = sampleId.map(SampleId), library = libId.map(LibraryId)), Duration.Inf) == 1 ReportPage( - List( - "Versions" -> Future(ReportPage(List(), - List(("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp"))), Map())) - ), + Nil, List("Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSingleFront.ssp")) ++ (if (krakenExecuted) List("Kraken analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp")) diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala index e523c6da4..2b7d5fd5c 100644 --- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala +++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MappingReport.scala @@ -37,6 +37,8 @@ object MappingReport extends ReportBuilder { /** Name of report */ val reportName = "Mapping Report" + def pipelineName = "mapping" + override def extFiles = super.extFiles ++ List("js/gears.js", "js/krona-2.0.js", "img/krona/loading.gif", "img/krona/hidden.png", "img/krona/favicon.ico") .map(x => ExtFile("/nl/lumc/sasc/biopet/pipelines/gears/report/ext/" + x, x)) @@ -53,11 +55,7 @@ object MappingReport extends ReportBuilder { Some(BammetricsReport.bamMetricsPage(summary, sampleId, libId)) } else None ReportPage((if (skipFlexiprep) Nil else List("QC" -> FlexiprepReport.flexiprepPage)) ::: - bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: List( - "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" - )), Map())), - "Files" -> Future(ReportPage(List(), Nil, Map())) - ) ::: + bamMetricsPage.map(_.subPages).getOrElse(Nil) ::: (if (krakenExecuted) List("Gears - Metagenomics" -> Future(ReportPage(List(), List( "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp" )), Map()))) diff --git a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala index 80bd73cb8..5ea93af19 100644 --- a/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala +++ b/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala @@ -79,10 +79,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { else Nil) ++ List("Reference" -> Future(ReportPage(List(), List( "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> pipelineName)) - ), Map())), - "Files" -> filesPage(), - "Versions" -> Future(ReportPage(List(), List("Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" - )), Map())) + ), Map())) ), List( "Report" -> frontSection) ++ @@ -113,32 +110,6 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { ) } - /** Files page, can be used general or at sample level */ - def filesPage(sampleId: Option[Int] = None, libraryId: Option[Int] = None): Future[ReportPage] = { - val dbFiles = summary.getFiles(runId, sample = sampleId.map(SampleId), - library = libraryId.map(LibraryId)) - .map(_.groupBy(_.pipelineId)) - val modulePages = dbFiles.map(_.map { - case (pipelineId, files) => - val moduleSections = files.groupBy(_.moduleId).map { - case (moduleId, files) => - val moduleName: Future[String] = moduleId match { - case Some(id) => summary.getModuleName(pipelineId, id).map(_.getOrElse("Pipeline")) - case _ => Future("Pipeline") - } - moduleName.map(_ -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> files))) - } - val moduleSectionsSorted = moduleSections.find(_._1 == "Pipeline") ++ moduleSections.filter(_._1 != "Pipeline") - summary.getPipelineName(pipelineId = pipelineId).map(_.get -> Future(ReportPage(Nil, Await.result(Future.sequence(moduleSectionsSorted), Duration.Inf).toList, Map()))) - }) - - val pipelineFiles = summary.getPipelineId(runId, pipelineName).flatMap(pipelinelineId => dbFiles.map(x => x(pipelinelineId.get).filter(_.moduleId.isEmpty))) - - modulePages.flatMap(Future.sequence(_)).map(x => ReportPage(x.toList, - s"$pipelineName files" -> ReportSection("/nl/lumc/sasc/biopet/core/report/files.ssp", Map("files" -> Await.result(pipelineFiles, Duration.Inf))) :: - "Sub pipelines/modules" -> ReportSection("/nl/lumc/sasc/biopet/core/report/fileModules.ssp", Map("pipelineIds" -> Await.result(dbFiles.map(_.keys.toList), Duration.Inf))) :: Nil, Map())) - } - /** Single sample page */ def samplePage(sampleId: Int, args: Map[String, Any]): Future[ReportPage] = Future { val krakenExecuted = Await.result(summary.getStatsSize(runId, "gearskraken", "krakenreport", @@ -161,9 +132,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future(ReportPage(List(), List( "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" )), Map()))) - else Nil) ++ - List("Files" -> filesPage(sampleId = sampleId) - ), List( + else Nil), List( "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("showPlot" -> true)), "Preprocessing" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true))) ++ @@ -195,7 +164,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { else Nil) ::: (if (krakenExecuted) List("Dustbin analysis" -> Future(ReportPage(List(), List( "Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp" )), Map()))) - else Nil) ::: List("Files" -> filesPage(sampleId = sampleId, libraryId = libId)), + 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")) -- GitLab