Commit a3009b39 authored by bow's avatar bow
Browse files

Unify output bam names

parent 9e62862f
...@@ -107,7 +107,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -107,7 +107,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
) )
/** File to add to the summary */ /** 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()) ++ "reference" -> referenceFasta()) ++
(if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map()) (if (input_R2.isDefined) Map("input_R2" -> input_R2.get) else Map())
......
...@@ -62,7 +62,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript ...@@ -62,7 +62,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
class Library(libId: String) extends AbstractLibrary(libId) { class Library(libId: String) extends AbstractLibrary(libId) {
def summaryFiles: Map[String, File] = (inputR1.map("input_R1" -> _) :: inputR2.map("input_R2" -> _) :: def summaryFiles: Map[String, File] = (inputR1.map("input_R1" -> _) :: inputR2.map("input_R2" -> _) ::
inputBam.map("input_bam" -> _) :: bamFile.map("output_bam" -> _) :: 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() def summaryStats: Map[String, Any] = Map()
...@@ -159,7 +159,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript ...@@ -159,7 +159,7 @@ trait MultisampleMappingTrait extends MultiSampleQScript
} }
def summaryFiles: Map[String, File] = (bamFile.map("output_bam" -> _) :: 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() def summaryStats: Map[String, Any] = Map()
......
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