Commit 77d06f6e authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Fix output bam files of mapping

parent 73995acb
...@@ -51,6 +51,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -51,6 +51,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
mapping.sampleId = Some(sampleId) mapping.sampleId = Some(sampleId)
mapping.libId = Some(libId) mapping.libId = Some(libId)
mapping.outputDir = libDir mapping.outputDir = libDir
mapping.outputName = sampleId + "-" + libId
(Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile)) (Some(mapping), Some(mapping.finalBamFile), preProcess(mapping.finalBamFile))
} }
...@@ -187,7 +188,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript { ...@@ -187,7 +188,7 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript {
val bamMetrics = new BamMetrics(root) val bamMetrics = new BamMetrics(root)
bamMetrics.sampleId = Some(sampleId) bamMetrics.sampleId = Some(sampleId)
bamMetrics.inputBam = preProcessBam.get bamMetrics.inputBam = preProcessBam.get
bamMetrics.outputDir = outputDir bamMetrics.outputDir = sampleDir
bamMetrics.init bamMetrics.init
bamMetrics.biopetScript bamMetrics.biopetScript
addAll(bamMetrics.functions) addAll(bamMetrics.functions)
......
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