Commit a952d8c4 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Convert mapping to sortsam for pipes

parent 9a3356a5
......@@ -337,10 +337,10 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val sortSam = new SortSam(this)
sortSam.output = output
if (config("use_pipes", default = true).asBoolean) {
val samtoolsSort = new SamtoolsSort(this)
samtoolsSort.outputFormat = Some("bam")
samtoolsSort.output = output
add(bwaCommand | samtoolsSort, chunking || !skipMarkduplicates)
//val samtoolsSort = new SamtoolsSort(this)
//samtoolsSort.outputFormat = Some("bam")
//samtoolsSort.output = output
add(bwaCommand | sortSam, chunking || !skipMarkduplicates)
} else {
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
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