From a3009b398e0f442c0142d7f1a6ef27b3474c3f48 Mon Sep 17 00:00:00 2001
From: bow <bow@bow.web.id>
Date: Fri, 15 Jan 2016 17:41:33 +0100
Subject: [PATCH] Unify output bam names
---
.../scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 2 +-
.../biopet/pipelines/mapping/MultisampleMappingTrait.scala | 4 ++--
2 files changed, 3 insertions(+), 3 deletions(-)
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 559c15ff3..a9be0fc1c 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -107,7 +107,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
)
/** File to add to the summary */
- def summaryFiles: Map[String, File] = Map("output_bamfile" -> finalBamFile, "input_R1" -> input_R1,
+ def summaryFiles: Map[String, File] = Map("output_bam" -> finalBamFile, "input_R1" -> input_R1,
"reference" -> referenceFasta()) ++
(if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
index 496ee2260..19348061d 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/MultisampleMappingTrait.scala
@@ -62,7 +62,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
class Library(libId: String) extends AbstractLibrary(libId) {
def summaryFiles: Map[String, File] = (inputR1.map("input_R1" -> _) :: inputR2.map("input_R2" -> _) ::
inputBam.map("input_bam" -> _) :: bamFile.map("output_bam" -> _) ::
- preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
+ preProcessBam.map("output_bam_preprocess" -> _) :: Nil).flatten.toMap
def summaryStats: Map[String, Any] = Map()
@@ -159,7 +159,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
}
def summaryFiles: Map[String, File] = (bamFile.map("output_bam" -> _) ::
- preProcessBam.map("output_preProcessBam" -> _) :: Nil).flatten.toMap
+ preProcessBam.map("output_bam_preprocess" -> _) :: Nil).flatten.toMap
def summaryStats: Map[String, Any] = Map()
--
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