From 7eb2bf8dee55b856a5721d37f231977a4c67db10 Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Tue, 2 Feb 2016 06:33:40 +0100
Subject: [PATCH] Fixed summary jobs
---
.../sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala | 2 ++
.../pipelines/gentrap/measures/CufflinksMeasurement.scala | 2 ++
.../biopet/pipelines/gentrap/measures/FragmentsPerGene.scala | 2 ++
3 files changed, 6 insertions(+)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
index d54fc2b33..ef1d47e45 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/BaseCounts.scala
@@ -67,5 +67,7 @@ class BaseCounts(val root: Configurable) extends QScript with Measurement with A
addTableAndHeatmap(jobs.values.map(_.strandedMetaExonCounts).toList, "strandedMetaExonCounts")
addTableAndHeatmap(jobs.values.map(_.strandedSenseMetaExonCounts).toList, "strandedSenseMetaExonCounts")
addTableAndHeatmap(jobs.values.map(_.strandedAntiSenseMetaExonCounts).toList, "strandedAntiSenseMetaExonCounts")
+
+ addSummaryJobs()
}
}
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 2d4f40973..26616991e 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
@@ -42,6 +42,8 @@ trait CufflinksMeasurement extends QScript with Measurement {
addHeatmapJob(mergeGenesFpkmTable, genesFpkmHeatmap, "genes_fpkm")
addHeatmapJob(mergeIsoFormFpkmTable, isoFormFpkmHeatmap, "iso_form_fpkm")
+
+ addSummaryJobs()
}
def mergeGenesFpkmTable: File = new File(outputDir, s"$name.genes.fpkm.tsv")
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
index 9ed01b496..e6323699e 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/measures/FragmentsPerGene.scala
@@ -32,6 +32,8 @@ class FragmentsPerGene(val root: Configurable) extends QScript with Measurement
addMergeTableJob(jobs.values.map(_.output).toList, mergedTable, "fragments_per_gene", s".$name.counts")
addHeatmapJob(mergedTable, heatmap, "fragments_per_gene")
+
+ addSummaryJobs()
}
def mergedTable = new File(outputDir, s"$name.fragments_per_gene.tsv")
--
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