Commit 9c5f43ad authored by bow's avatar bow
Browse files

Fix errors caused by merging

parent 5db19c93
......@@ -29,7 +29,7 @@ class CustomVarScan(val root: Configurable) extends BiopetCommandLineFunction {
// mpileup, varscan, fix_mpileup.py, binom_test.py, bgzip, tabix
private def mpileup = new SamtoolsMpileup(wrapper.root) {
this.input = wrapper.input
this.input = List(wrapper.input)
disableBaq = true
reference = config("reference")
depth = Option(1000000)
......
......@@ -156,7 +156,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
add(baiLn)
val bamLn = Ln(qscript, oldBamFile, bamFile.get)
bamLn.deps :+= baiLn.out
bamLn.deps :+= baiLn.output
add(bamLn)
}
......@@ -197,7 +197,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
add(baiLn)
val bamLn = Ln(qscript, input.head, bamFile)
bamLn.deps :+= baiLn.out
bamLn.deps :+= baiLn.output
add(bamLn)
Some(bamFile)
} else {
......
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