From 12da6e968b16a0ad59ac636b63d467c8a6453969 Mon Sep 17 00:00:00 2001
From: Sander van der Zeeuw <s.a.j.van_der_zeeuw@lumc.nl>
Date: Thu, 16 Jul 2015 16:56:24 +0200
Subject: [PATCH] Fix symlinking of the final bai file
---
.../nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala | 6 +++---
.../nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala | 2 +-
2 files changed, 4 insertions(+), 4 deletions(-)
diff --git a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
index 024789e25..27d5f9f08 100644
--- a/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
+++ b/public/gentrap/src/main/scala/nl/lumc/sasc/biopet/pipelines/gentrap/Gentrap.scala
@@ -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 {
diff --git a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
index 40eb6faca..7eb06d619 100644
--- a/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
+++ b/public/mapping/src/main/scala/nl/lumc/sasc/biopet/pipelines/mapping/Mapping.scala
@@ -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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