diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp index 944c9fbdbe0dfef49d3d840dd399945a77df00c2..3b7b02727ee1c930e3af48f9b0d37d0278bc3f8c 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/rnaHistogram.ssp @@ -1,4 +1,5 @@ -#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._) +#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) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._) @@ -72,14 +73,14 @@ case _ => allLibraries.filter(_.sampleId == sample.id).map(x => Some(x.id)).toList } }# - ${sample} + ${sample.name} #for (libId <- libs) #{ val libName = libId.map(l => allLibraries.find(_.id == l).get.name) }# #if (libs.head != libId) #end #if (!sampleLevel) ${libName} #end #{ val statsPaths = fields.map(x => x -> List("metrics", x.toUpperCase)).toMap - val results = summary.getStatKeys(runId, "bammetrics", "wgs", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths) + val results = summary.getStatKeys(runId, "bammetrics", "rna", sample = sample.id, library = libId.map(LibraryId).getOrElse(NoLibrary), keyValues = statsPaths) }# #for (field <- fields) ${results(field)} diff --git a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp index ea2e2dab1f7f78a4dc665d3ab3b011dad8983b8b..3e0147e89c94eb6e6239e56ccc5dc61c0b1c804a 100644 --- a/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp +++ b/bammetrics/src/main/resources/nl/lumc/sasc/biopet/pipelines/bammetrics/wgsHistogram.ssp @@ -1,4 +1,5 @@ -#import(nl.lumc.sasc.biopet.utils.summary.db.Schema._) +#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) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb._) #import(nl.lumc.sasc.biopet.utils.summary.db.SummaryDb.Implicts._) 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 a7929e471f6ad5dbef277600a9d3fbab7375ea60..f5eb76650c0fa8a268808ea3fed4fbf61dd6016b 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 @@ -306,12 +306,12 @@ object BammetricsReport extends ReportBuilder { sampleId: Option[Int] = None, libraryId: Option[Int] = None): Unit = { val statsPaths = Map( - "position" -> List("rna", "histogram", "normalized_position"), - "count" -> List("rna", "histogram", "All_Reads.normalized_coverage") + "position" -> List("histogram", "normalized_position"), + "count" -> List("histogram", "All_Reads.normalized_coverage") ) writePlotFromSummary(outputDir, prefix, summary, libraryLevel, sampleId, libraryId, statsPaths, - "coverage", "count", "bammetrics", "rna", + "position", "count", "bammetrics", "rna", "Relative position", "Coverage", "Rna coverage") } diff --git a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala index f24feb43cd6697f8d77e899b54ea3819e7acf7bd..63773032def8c6650faaec9191a09c0b9de3b872 100644 --- a/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala +++ b/biopet-utils/src/main/scala/nl/lumc/sasc/biopet/utils/summary/db/SummaryDb.scala @@ -251,6 +251,9 @@ trait SummaryDb extends Closeable { library: LibraryQuery = NoLibrary, keyValues: Map[String, List[String]]): Map[String, Option[Any]] = { val stats = Await.result(getStat(runId, pipeline, module, sample, library), Duration.Inf) + if (module == ModuleName("rna")) { + "" + } keyValues.map { case (key, path) => stats match {