Commit c8992164 authored by Peter van 't Hof's avatar Peter van 't Hof
Browse files

Adding comments

parent b5c021d7
......@@ -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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