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biopet.biopet
Commit b14d290d authored by Wai Yi Leung's avatar Wai Yi Leung
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Add mergejob

parent 07c70b86
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Showing with 6 additions and 5 deletions
public/gears/src/main/scala/nl/lumc/sasc/biopet/pipelines/gears/GearsTrait.scala
View file @ b14d290d
...@@ -251,11 +251,12 @@ trait GearsTrait extends MultiSampleQScript with SummaryQScript { qscript => ...@@ -251,11 +251,12 @@ trait GearsTrait extends MultiSampleQScript with SummaryQScript { qscript =>
if (inFiles.size == 1) inFiles.head if (inFiles.size == 1) inFiles.head
else { else {
val mergedBam = createFile(".merged.bam") val mergedBam = createFile(".merged.bam")
val job = new MergeSamFiles(qscript) val mergejob = new MergeSamFiles(qscript)
job.input = inFiles mergejob.input = inFiles
job.output = mergedBam mergejob.output = mergedBam
job.sortOrder = mergeSortOrder mergejob.sortOrder = mergeSortOrder
job.output add(mergejob)
mergejob.output
} }
} }
......
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