Commit 6d3728a0 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Merge branch 'fix-baiFileSymlink' into 'develop'

Fix symlinking of the final bai file

Fixes FinalBai file symlinking

See merge request !195
parents 9f8ceae0 12da6e96
......@@ -720,12 +720,12 @@ class Gentrap(val root: Configurable) extends QScript
if (inFiles.size == 1) {
val jobBam = new Ln(qscript)
jobBam.input = inFiles.head
jobBam.input = inFiles.head.getAbsoluteFile
jobBam.output = outFile
val jobIdx = new Ln(qscript)
jobIdx.input = swapExt(jobBam.input, ".bam", ".bai")
jobIdx.output = swapExt(jobBam.output, ".bam", ".bai")
jobIdx.input = swapExt(libraries.values.head.libDir, jobBam.input, ".bam", ".bai")
jobIdx.output = swapExt(sampleDir, jobBam.output, ".bam", ".bai")
CombineFileJobSet(jobBam, Some(jobIdx))
} else {
......@@ -268,7 +268,7 @@ class Mapping(val root: Configurable) extends QScript with SummaryQScript with S
add(Ln(this, swapExt(outputDir, bamFile, ".bam", ".bai"), swapExt(outputDir, finalBamFile, ".bam", ".bai")))
add(Ln(this, bamFile, finalBamFile))
outputFiles += ("finalBamFile" -> bamFile)
outputFiles += ("finalBamFile" -> finalBamFile.getAbsoluteFile)
if (config("generate_wig", default = false).asBoolean)
addAll(Bam2Wig(this, finalBamFile).functions)
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