Commit 86cc3923 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Change to flatmap

parent 3828a150
...@@ -480,7 +480,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S ...@@ -480,7 +480,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
reorderSam.input = ar._2 reorderSam.input = ar._2
reorderSam.output = output reorderSam.output = output
val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: (if (paired) zcatR2.get._1 else None) :: val pipe = new BiopetFifoPipe(this, (zcatR1._1 :: zcatR2.flatMap(_._1) ::
Some(starCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten) Some(starCommand) :: Some(ar._1) :: Some(reorderSam) :: Nil).flatten)
pipe.threadsCorrection = -3 pipe.threadsCorrection = -3
zcatR1._1.foreach(x => pipe.threadsCorrection -= 1) zcatR1._1.foreach(x => pipe.threadsCorrection -= 1)
......
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