Commit 8c75f931 authored by Wai Yi Leung's avatar Wai Yi Leung
Browse files

Merge branch 'fix-basecounter_executable' into 'develop'

Fix basecounter executable



See merge request !341
parents b3e8c237 be7e4e74
......@@ -31,6 +31,7 @@ object BiopetToolsExecutable extends BiopetExecutable {
nl.lumc.sasc.biopet.tools.VcfToTsv,
nl.lumc.sasc.biopet.tools.VcfFilter,
nl.lumc.sasc.biopet.tools.VcfStats,
nl.lumc.sasc.biopet.tools.BaseCounter,
nl.lumc.sasc.biopet.tools.FindRepeatsPacBio,
nl.lumc.sasc.biopet.tools.MpileupToVcf,
nl.lumc.sasc.biopet.tools.FastqSplitter,
......
......@@ -104,7 +104,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
)), Map()))
else Nil) ++
List("Files" -> filesPage
), List(
), 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))) ++
......@@ -122,10 +122,10 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
ReportPage(
("Alignment" -> BammetricsReport.bamMetricsPage(summary, Some(sampleId), Some(libId))) ::
(if (flexiprepExecuted) List("QC" -> FlexiprepReport.flexiprepPage) else Nil) :::
(if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
"Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
else Nil),
(if (krakenExecuted) List("Dustbin analysis" -> ReportPage(List(), List(
"Krona Plot" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/gears/krakenKrona.ssp"
)), Map()))
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"))
......
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