From dd71e82bb9b385bab8ff654b710f9341c3a36a0f Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Mon, 25 Jan 2016 13:41:10 +0100
Subject: [PATCH] Added tables and heatmaps to summary
---
.../pipelines/gentrap/measures/CufflinksMeasurement.scala | 4 ++--
.../pipelines/gentrap/measures/FragmentsPerGene.scala | 2 +-
.../biopet/pipelines/gentrap/measures/Measurement.scala | 7 ++++++-
3 files changed, 9 insertions(+), 4 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
index 229d78e65..95b9df1e4 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/CufflinksMeasurement.scala
@@ -22,8 +22,8 @@ trait CufflinksMeasurement extends QScript with Measurement {
id -> cufflinks
}
- addMergeTableJob(jobs.values.map(_.outputGenesFpkm).toList, mergeGenesFpkmTable)
- addMergeTableJob(jobs.values.map(_.outputIsoformsFpkm).toList, mergeIsoFormFpkmTable)
+ addMergeTableJob(jobs.values.map(_.outputGenesFpkm).toList, mergeGenesFpkmTable, "genes_fpkm")
+ addMergeTableJob(jobs.values.map(_.outputIsoformsFpkm).toList, mergeIsoFormFpkmTable, "iso_form")
addHeatmapJob(mergeGenesFpkmTable, genesFpkmHeatmap, "genes_fpkm")
addHeatmapJob(mergeIsoFormFpkmTable, isoFormFpkmHeatmap, "iso_form_fpkm")
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index 440dc1246..34664e374 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -28,7 +28,7 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
id -> job
}
- addMergeTableJob(jobs.values.map(_.output).toList, mergedTable)
+ addMergeTableJob(jobs.values.map(_.output).toList, mergedTable, "fragments_per_gene")
addHeatmapJob(mergedTable, heatmap, "fragments_per_gene")
}
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
index f09cc09f6..8e6a5bbd6 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/Measurement.scala
@@ -36,11 +36,15 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require(bamFiles.nonEmpty)
}
+ private var extraSummaryFiles: Map[String, File] = Map()
+
def addMergeTableJob(countFiles: List[File],
outputFile: File,
+ name: String,
args: MergeArgs = mergeArgs): Unit = {
add(MergeTables(this, countFiles, outputFile,
args.idCols, args.valCol, args.numHeaderLines, args.fallback))
+ extraSummaryFiles += s"${name}_table" -> outputFile
}
def addHeatmapJob(countTable: File, outputFile: File, name: String): Unit = {
@@ -49,13 +53,14 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
job.output = outputFile
job.countType = Some(name)
add(job)
+ extraSummaryFiles += s"${name}_heatmap" -> outputFile
}
/** Must return a map with used settings for this pipeline */
def summarySettings: Map[String, Any] = Map()
/** File to put in the summary for thie pipeline */
- def summaryFiles: Map[String, File] = Map() ++ bamFiles.map { case (id, file) => s"input_bam_$id" -> file }
+ def summaryFiles: Map[String, File] = extraSummaryFiles ++ bamFiles.map { case (id, file) => s"input_bam_$id" -> file }
/** Name of summary output file */
def summaryFile: File = new File(outputDir, s"$name.summary.json")
--
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