Commit cfd74de0 authored by bow's avatar bow

Fix missing read group assignment for GSNAP and TopHat

parent 68d7fab7
......@@ -346,12 +346,12 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
val sortSam = new SortSam(this)
sortSam.input = gsnapCommand.output
sortSam.output = output
sortSam.output = swapExt(output.getParent, output, ".bam", ".sorted.bam")
sortSam.sortOrder = "coordinate"
sortSam.isIntermediate = chunking || !skipMarkduplicates
add(sortSam)
sortSam.output
addAddOrReplaceReadGroups(sortSam.output, output)
}
def addTophat(R1: File, R2: File, output: File, deps: List[File]): File = {
......@@ -368,19 +368,14 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
tophat.no_convert_bam = false
add(tophat)
val ln = new Ln(this)
ln.input = tophat.outputAcceptedHits
ln.output = swapExt(output.getParent, output, ".bam", ".raw.bam")
add(ln)
val sortSam = new SortSam(this)
sortSam.input = ln.output
sortSam.output = output
sortSam.input = tophat.outputAcceptedHits
sortSam.output = swapExt(output.getParent, output, ".bam", ".sorted.bam")
sortSam.sortOrder = "coordinate"
sortSam.isIntermediate = chunking || !skipMarkduplicates
add(sortSam)
sortSam.output
addAddOrReplaceReadGroups(sortSam.output, output)
}
/**
* Adds stampy jobs
......
Markdown is supported
0% or
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment