Commit 0b3c1e25 authored by Peter van 't Hof's avatar Peter van 't Hof

Make readgroup_library a config value

parent 74845bd6
......@@ -86,6 +86,9 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
/** Readgroup sequencing center */
protected var readgroupSequencingCenter: Option[String] = config("readgroup_sequencing_center")
/** Readgroup library */
protected var readgroupLibrary: Option[String] = config("readgroup_library")
/** Readgroup description */
protected var readgroupDescription: Option[String] = config("readgroup_description")
......@@ -572,7 +575,7 @@ class Mapping(val parent: Configurable) extends QScript with SummaryQScript with
/** Returns readgroup for bwa */
def getReadGroupBwa: String = {
var RG: String = "@RG\\t" + "ID:" + readgroupId + "\\t"
RG += "LB:" + libId.get + "\\t"
readgroupLibrary.foreach(lb => RG += "LB:" + lb + "\\t")
RG += "PL:" + platform + "\\t"
platformUnit.foreach(x => RG += "PU:" + x + "\\t")
RG += "SM:" + sampleId.get + "\\t"
......
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