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 e16eff14c6770f0ee36c8657aa2b182ba8ee3320..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 @@ -32,4 +32,6 @@ 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/GentrapReport.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/GentrapReport.scala index 497638604ee15cf28b4e4e7b91fda5d24e3399fa..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 @@ -34,4 +34,6 @@ object GentrapReport extends MultisampleMappingReportTrait { /** 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/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingReport.scala index 86e16cd0dc6e1e9b05cdc605ea7cb31b0a6997b4..71ef4e48a2002fa002e069ef2bac012795c3f96d 100644 --- 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 @@ -21,20 +21,21 @@ 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 = { - //Source.fromInputStream(getClass.getResourceAsStream("/nl/lumc/sasc/biopet/pipelines/carp/carpFont.ssp")).foreach(print(_)) ReportPage( List("Samples" -> generateSamplesPage(pageArgs)) ++ Map("Reference" -> ReportPage(List(), List( - "Reference" -> ReportSection("/nl/lumc/sasc/biopet/core/report/reference.ssp", Map("pipeline" -> "shiva")) + "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" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/carp/carpFront.ssp"), + "Report" -> frontSection, "Alignment" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/bammetrics/alignmentSummary.ssp", Map("sampleLevel" -> true, "showPlot" -> true, "showTable" -> false) ), @@ -57,7 +58,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder { "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()) + Map("pipelineName" -> pipelineName, "fileTag" -> "preProcessBam"))), Map()) /** Single sample page */ def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = { 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 c39782d6e80003b67273074c922313256536661c..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 @@ -42,6 +42,8 @@ object ShivaReport extends MultisampleMappingReportTrait { 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))