Commit 139c0d7b authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

No piping anymore

parent 3ef9d275
......@@ -165,7 +165,10 @@ trait MultisampleMappingTrait extends MultiSampleQScript
if (!readGroupOke && correctReadgroups && !dictOke && correctDict) {
logger.info("Correcting readgroups and sequence dictionary, file:" + inputBam.get)
add(reorder | aorrg)
aorrg.output = swapExt(bamFile.get.getParentFile, bamFile.get, ".bam", ".aorrg.bam")
add(aorrg)
reorder.input = aorrg.output
add(reorder)
} else if (!readGroupOke && correctReadgroups) {
logger.info("Correcting readgroups, file:" + inputBam.get)
qscript.add(aorrg)
......
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