Commit 4b348b21 authored by bow's avatar bow
Browse files

Update gentrap summary and stats

parent 0c25f894
...@@ -244,9 +244,15 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi ...@@ -244,9 +244,15 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
def summaryFile: File = new File(outputDir, "gentrap.summary.json") def summaryFile: File = new File(outputDir, "gentrap.summary.json")
/** Files that will be listed in the summary file */ /** Files that will be listed in the summary file */
def summaryFiles: Map[String, File] = def summaryFiles: Map[String, File] = Map(
"annotation_refflat" -> annotationRefFlat
) ++ Map(
"annotation_gtf" -> annotationGtf,
"annotation_bed" -> annotationBed,
"ribosome_refflat" -> ribosomalRefFlat
).collect { case (key, Some(value)) => key -> value } ++
mergeTableJobs.collect { case (key, Some(value)) => key -> value.output } ++ mergeTableJobs.collect { case (key, Some(value)) => key -> value.output } ++
heatmapJobs.collect { case (key, Some(value)) => key -> value.output } heatmapJobs.collect { case (key, Some(value)) => key -> value.output }
/** Statistics shown in the summary file */ /** Statistics shown in the summary file */
def summaryStats: Map[String, Any] = Map() def summaryStats: Map[String, Any] = Map()
...@@ -254,14 +260,12 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi ...@@ -254,14 +260,12 @@ class Gentrap(val root: Configurable) extends QScript with MultiSampleQScript wi
/** Pipeline settings shown in the summary file */ /** Pipeline settings shown in the summary file */
def summarySettings: Map[String, Any] = Map( def summarySettings: Map[String, Any] = Map(
"aligner" -> aligner, "aligner" -> aligner,
"expression_measures" -> expMeasures.map(_.toString), "expression_measures" -> expMeasures.toList.map(_.toString),
"strand_protocol" -> strandProtocol, "strand_protocol" -> strandProtocol.toString,
"annotation_refflat" -> annotationRefFlat, "call_variants" -> callVariants,
"remove_ribosomal_reads" -> removeRibosomalReads,
"version" -> version "version" -> version
) ++ Map( )
"annotation_gtf" -> annotationGtf,
"annotation_bed" -> annotationBed
).collect { case (key, Some(value)) => key -> value }
/** Job for writing PDF report template */ /** Job for writing PDF report template */
protected lazy val pdfTemplateJob: PdfReportTemplateWriter = { protected lazy val pdfTemplateJob: PdfReportTemplateWriter = {
......
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