Commit acf6fe14 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-renames' into 'develop'

Fix renames

Some naming fixes for consistency.

See merge request !309
parents 9e62862f 793a34eb
......@@ -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())
......
......@@ -66,7 +66,7 @@ trait MultisampleMappingReportTrait extends MultisampleReportBuilder {
"After QC fastq files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/flexiprep/flexiprepOutputfiles.ssp"),
"Bam files per lib" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp", Map("sampleLevel" -> false)),
"Preprocessed bam files" -> ReportSection("/nl/lumc/sasc/biopet/pipelines/mapping/outputBamfiles.ssp",
Map("pipelineName" -> pipelineName, "fileTag" -> "preProcessBam"))), Map())
Map("pipelineName" -> pipelineName, "fileTag" -> "output_bam_preprocess"))), Map())
/** Single sample page */
def samplePage(sampleId: String, args: Map[String, Any]): ReportPage = {
......
......@@ -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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