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