Commit fa4b60f8 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fixed typo

parent 4143a145
......@@ -58,9 +58,9 @@ trait MultisampleMappingTrait extends MultiSampleQScript
def summaryStats: Map[String, Any] = Map()
lazy val inputR1: Option[File] = MultisampleMapping.fileMustBeAbsulute(config("R1"))
lazy val inputR2: Option[File] = MultisampleMapping.fileMustBeAbsulute(config("R2"))
lazy val inputBam: Option[File] = MultisampleMapping.fileMustBeAbsulute(if (inputR1.isEmpty) config("bam") else None)
lazy val inputR1: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R1"))
lazy val inputR2: Option[File] = MultisampleMapping.fileMustBeAbsolute(config("R2"))
lazy val inputBam: Option[File] = MultisampleMapping.fileMustBeAbsolute(if (inputR1.isEmpty) config("bam") else None)
lazy val bamToFastq: Boolean = config("bam_to_fastq", default = false)
lazy val correctReadgroups: Boolean = config("correct_readgroups", default = false)
......@@ -207,7 +207,7 @@ object MultisampleMapping extends PipelineCommand {
val None, MergeSam, MarkDuplicates, PreProcessMergeSam, PreProcessMarkDuplicates = Value
def fileMustBeAbsulute(file: Option[File]): Option[File] = {
def fileMustBeAbsolute(file: Option[File]): Option[File] = {
if (file.forall(_.isAbsolute)) file
else {
Logging.addError(s"$file should be a absolute file path")
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