Commit 23a0b18f authored by pjvan_thof's avatar pjvan_thof
Browse files

No merging with only 1 sample

parent 532f837c
...@@ -80,7 +80,7 @@ class Star(val parent: Configurable) ...@@ -80,7 +80,7 @@ class Star(val parent: Configurable)
var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases") var genomeSAindexNbases: Option[Long] = config("genomesaindexnbases")
var genomeSAsparseD: Option[Int] = config("genomesasparsed") var genomeSAsparseD: Option[Int] = config("genomesasparsed")
val defaultGtf: Option[File] = config("annotation_gtf") private def defaultGtf: Option[File] = config("annotation_gtf")
@Input(required = false) @Input(required = false)
var sjdbGTFfile: Option[File] = defaultGtf match { var sjdbGTFfile: Option[File] = defaultGtf match {
case Some(file) => config("sjdbgtfile", default = file) case Some(file) => config("sjdbgtfile", default = file)
......
...@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript => ...@@ -54,7 +54,7 @@ trait Measurement extends SummaryQScript with Reference { qscript: QScript =>
require(bamFiles.nonEmpty) require(bamFiles.nonEmpty)
} }
lazy val mergeCountFiles: Boolean = config("merge_count_files", default = true) lazy val mergeCountFiles: Boolean = config("merge_count_files", default = bamFiles.size > 1)
private var extraSummaryFiles: Map[String, File] = Map() private var extraSummaryFiles: Map[String, File] = Map()
......
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