Commit bb300878 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Moved sam file

parent 4abe2a58
......@@ -333,7 +333,6 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
if (paired) bwaCommand.R2 = R2.get
bwaCommand.deps = deps
bwaCommand.R = Some(getReadGroupBwa)
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
bwaCommand.isIntermediate = true
if (config("use_pipes", default = true).asBoolean) {
val samtoolsSort = new SamtoolsSort(this)
......@@ -341,6 +340,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
samtoolsSort.output = output
add(bwaCommand | samtoolsSort)
} else {
bwaCommand.output = swapExt(output.getParent, output, ".bam", ".sam")
add(bwaCommand)
val sortSam = SortSam(this, bwaCommand.output, output)
if (chunking || !skipMarkduplicates) sortSam.isIntermediate = true
......
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