Commit 3584a778 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Saver execution order

parent f95a231c
......@@ -280,9 +280,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
} else None
lazy val svCalling = if (config("sv_calling", default = false).asBoolean) {
val svCalling = new ShivaSvCalling(this)
samples.foreach(x => x._2.preProcessBam.foreach(bam => svCalling.addBamFile(bam, Some(x._1))))
Some(svCalling)
Some(new ShivaSvCalling(this))
} else None
/** This will add the mutisample variantcalling */
......@@ -298,6 +296,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
svCalling.foreach(sv => {
sv.outputDir = new File(outputDir, "sv_calling")
samples.foreach(x => x._2.preProcessBam.foreach(bam => sv.addBamFile(bam, Some(x._1))))
sv.init()
sv.biopetScript()
addAll(sv.functions)
......
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