From c899216488cda4850b7f63b89f0f66d74e96ae8b Mon Sep 17 00:00:00 2001
From: Peter van 't Hof <p.j.van_t_hof@lumc.nl>
Date: Wed, 11 May 2016 20:52:26 +0200
Subject: [PATCH] Adding comments
---
.../scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala | 3 +++
1 file changed, 3 insertions(+)
diff --git a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
index d7c40fb76..6d4484976 100644
--- a/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
+++ b/generate-indexes/src/main/scala/nl/lumc/sasc/biopet/pipelines/GenerateIndexes.scala
@@ -220,6 +220,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
outputConfig += "gsnap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
outputConfig += "gmap" -> Map("dir" -> gmapBuild.dir.getAbsolutePath, "db" -> genomeName)
+ // STAR index
val starDir = new File(genomeDir, "star")
val starIndex = new Star(this)
starIndex.outputDir = starDir
@@ -232,6 +233,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
"genomeDir" -> starDir.getAbsolutePath
)
+ // Bowtie index
val bowtieIndex = new BowtieBuild(this)
bowtieIndex.reference = createLinks(new File(genomeDir, "bowtie"))
bowtieIndex.baseName = "reference"
@@ -239,6 +241,7 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
configDeps :+= bowtieIndex.jobOutputFile
outputConfig += "bowtie" -> Map("reference_fasta" -> bowtieIndex.reference.getAbsolutePath)
+ // Bowtie2 index
val bowtie2Index = new Bowtie2Build(this)
bowtie2Index.reference = createLinks(new File(genomeDir, "bowtie2"))
bowtie2Index.baseName = "reference"
--
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