diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp index 31b67ba3d791ba6b945892891f860560557b8baa..21feab6c9121849c634a39756c6beff7b2c7ef24 100644 --- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp +++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp @@ -1,11 +1,11 @@ -#import(nl.lumc.sasc.biopet.core.summary.Summary) +#import(nl.lumc.sasc.biopet.utils.summary.Summary) #import(nl.lumc.sasc.biopet.core.report.ReportPage) <%@ var summary: Summary %> <%@ var rootPath: String %> - + diff --git a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp index 690c5e3e722c480a51d07599943d574d0f4eb1b8..8e9761cdd27d1354c45d11082aff6fc86f298efa 100644 --- a/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp +++ b/public/gears/src/main/resources/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp @@ -1,6 +1,4 @@ -#import(nl.lumc.sasc.biopet.core.summary.Summary) -#import(nl.lumc.sasc.biopet.core.report.ReportPage) -#import(nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport) +#import(nl.lumc.sasc.biopet.utils.summary.Summary) #import(java.io.File) <%@ var summary: Summary %> <%@ var sampleId: Option[String] = None %> @@ -19,63 +17,42 @@ val librariesCount = summary.samples.foldLeft(0)(_ + summary.libraries(_).size) }# - - - - - - -

Root

-
- - - - - -
- - - - - -
- -
- - #if (showIntro)
-
- <%--
--%> -

- #if (sampleId.isDefined && libId.isDefined) - Here we show aggregated quality statistics sequencing library ${libId} for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads. - #elseif (sampleId.isDefined) - Here we show aggregated quality statistics for every sequencing library for sample ${sampleId}. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads. - #else - Here we show aggregated quality statistics for every sequencing library. It shows the total number of bases used after quality control, and the total number of bases discarded during quality control. This is done for both forward and reverse reads. - #end -

-
+
+
+ Here we show a sunburst visualisation of the analysis of the metagenome in sample: ${sampleId} +
+
#end #if (showPlot) - #{ - -// FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R1","R1", summary, sampleId = sampleId) -// FlexiprepReport.baseSummaryPlot(outputDir, "QC_Bases_R2","R2", summary, sampleId = sampleId) - - }# -
- -
- - -
- -
+
+ + + + + + +

Root

+
+ - + - + +
+ +
+ + + +
+ +
+
#end diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala index f67b1b8fcf8dc4561682b1014ab1609e4b390408..9362fde726824639ac2c16119759498071bd1b25 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/Gears.scala @@ -25,8 +25,7 @@ import nl.lumc.sasc.biopet.utils.config.Configurable import org.broadinstitute.gatk.queue.QScript /** - * This is a trait for the Gears pipeline - * The ShivaTrait is used as template for this pipeline + * Created by wyleung */ class Gears(val root: Configurable) extends QScript with SummaryQScript { qscript => @@ -44,7 +43,7 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { @Argument(required = false) var outputName: String = _ - var GearsOutputFiles: Map[String, File] = Map.empty + var GearsOutputFiles: scala.collection.mutable.Map[String, File] = scala.collection.mutable.Map.empty /** Executed before running the script */ def init(): Unit = { @@ -61,6 +60,12 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { } } + override def reportClass = { + val gears = new GearsReport(this) + gears.outputDir = new File(outputDir, "report") + gears.summaryFile = summaryFile + Some(gears) + } /** Method to add jobs */ def biopetScript(): Unit = { @@ -96,9 +101,9 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { fastqSync.outputStats = new File(outputDir, s"$outputName.sync.stats.json") add(fastqSync) - GearsOutputFiles ++ Map("fastqsync_stats" -> fastqSync.outputStats) - GearsOutputFiles ++ Map("fastqsync_R1" -> fastqSync.outputFastq1) - GearsOutputFiles ++ Map("fastqsync_R2" -> fastqSync.outputFastq2) + GearsOutputFiles += ("fastqsync_stats" -> fastqSync.outputStats) + GearsOutputFiles += ("fastqsync_R1" -> fastqSync.outputFastq1) + GearsOutputFiles += ("fastqsync_R2" -> fastqSync.outputFastq2) List(fastqSync.outputFastq1, fastqSync.outputFastq2) }.getOrElse(List(fastqFileR1, fastqFileR2).flatten) @@ -114,9 +119,9 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { krakenAnalysis.unclassified_out = Option(new File(outputDir, s"$outputName.krkn.unclassified.fastq")) add(krakenAnalysis) - GearsOutputFiles ++ Map("kraken_output_raw" -> krakenAnalysis.output) - GearsOutputFiles ++ Map("kraken_classified_out" -> krakenAnalysis.classified_out) - GearsOutputFiles ++ Map("kraken_unclassified_out" -> krakenAnalysis.unclassified_out) + GearsOutputFiles += ("kraken_output_raw" -> krakenAnalysis.output) + GearsOutputFiles += ("kraken_classified_out" -> krakenAnalysis.classified_out.getOrElse("")) + GearsOutputFiles += ("kraken_unclassified_out" -> krakenAnalysis.unclassified_out.getOrElse("")) // create kraken summary file @@ -126,8 +131,8 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { krakenReport.output = new File(outputDir, s"$outputName.krkn.full") add(krakenReport) - GearsOutputFiles ++ Map("kraken_report_input" -> krakenReport.input) - GearsOutputFiles ++ Map("kraken_report_output" -> krakenReport.output) + GearsOutputFiles += ("kraken_report_input" -> krakenReport.input) + GearsOutputFiles += ("kraken_report_output" -> krakenReport.output) val krakenReportJSON = new KrakenReportToJson(qscript) krakenReportJSON.inputReport = krakenReport.output @@ -135,10 +140,10 @@ class Gears(val root: Configurable) extends QScript with SummaryQScript { krakenReportJSON.skipNames = config("skipNames", default = false) add(krakenReportJSON) - addSummaryJobs() + GearsOutputFiles += ("kraken_report_json_input" -> krakenReportJSON.inputReport) + GearsOutputFiles += ("kraken_report_json_output" -> krakenReportJSON.output) - GearsOutputFiles ++ Map("kraken_report_json_input" -> krakenReportJSON.inputReport) - GearsOutputFiles ++ Map("kraken_report_json_output" -> krakenReportJSON.output) + addSummaryJobs() } /** Location of summary file */ diff --git a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala index 7fc93225e5fae6aa245acb02d95c01f4041a4720..02a2684c368be7cd63ddeb26f334f1a73767a86e 100644 --- a/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala +++ b/public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsReport.scala @@ -2,16 +2,11 @@ package nl.lumc.sasc.biopet.pipelines.gears import java.io.{ PrintWriter, File } -import nl.lumc.sasc.biopet.core.config.Configurable import nl.lumc.sasc.biopet.core.report.MultisampleReportBuilder import nl.lumc.sasc.biopet.core.report.ReportBuilderExtension import nl.lumc.sasc.biopet.core.report.ReportPage import nl.lumc.sasc.biopet.core.report.ReportSection -import nl.lumc.sasc.biopet.core.report._ -import nl.lumc.sasc.biopet.core.summary.{ SummaryValue, Summary } -import nl.lumc.sasc.biopet.extensions.rscript.StackedBarPlot -import nl.lumc.sasc.biopet.pipelines.bammetrics.BammetricsReport -import nl.lumc.sasc.biopet.pipelines.flexiprep.FlexiprepReport +import nl.lumc.sasc.biopet.utils.config.Configurable class GearsReport(val root: Configurable) extends ReportBuilderExtension { val builder = GearsReport @@ -30,58 +25,29 @@ object GearsReport extends MultisampleReportBuilder { def indexPage = { ReportPage( List("Samples" -> generateSamplesPage(pageArgs)) ++ - Map("Files" -> filesPage, + Map( "Versions" -> ReportPage(List(), List(( "Executables" -> ReportSection("/nl/lumc/sasc/biopet/core/report/executables.ssp" ))), Map()) ), List( - "Report" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.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)) + "Gears intro" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsFront.ssp"), + "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp") ), pageArgs ) } - def filesPage = 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" -> "gears", "fileTag" -> "preProcessBam")) - ), Map()) - def samplePage(sampleId: String, args: Map[String, Any]) = { 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"), "Sunburst analysis" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/gearsSunburst.ssp") ), args) } def libraryPage(sampleId: String, libId: String, args: Map[String, Any]) = { 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) }
PipelineShiva
PipelineGears
Version${summary.getValue("meta", "pipeline_version")}
Last commit hash${summary.getValue("meta", "last_commit_hash")}
Output directory${summary.getValue("meta", "output_dir")}