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Commit 46f8b1b5 authored by Peter van 't Hof's avatar Peter van 't Hof
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Change to compressed output

parent 43a4bc76
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public/shiva/src/main/scala/nl/lumc/sasc/biopet/pipelines/shiva/ShivaTrait.scala
View file @ 46f8b1b5
...@@ -144,8 +144,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference { ...@@ -144,8 +144,8 @@ trait ShivaTrait extends MultiSampleQScript with SummaryQScript with Reference {
config("bam_to_fastq", default = false).asBoolean match { config("bam_to_fastq", default = false).asBoolean match {
case true => case true =>
val samToFastq = SamToFastq(qscript, config("bam"), val samToFastq = SamToFastq(qscript, config("bam"),
new File(libDir, sampleId + "-" + libId + ".R1.fastq"), new File(libDir, sampleId + "-" + libId + ".R1.fq.gz"),
new File(libDir, sampleId + "-" + libId + ".R2.fastq")) new File(libDir, sampleId + "-" + libId + ".R2.fq.gz"))
samToFastq.isIntermediate = true samToFastq.isIntermediate = true
qscript.add(samToFastq) qscript.add(samToFastq)
mapping.foreach(mapping => { mapping.foreach(mapping => {
......
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