Commit 91af94b8 authored by Peter van 't Hof's avatar Peter van 't Hof

Fixing config files

parent bf2a496b
......@@ -108,7 +108,10 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
bowtieIndex.baseName = "reference"
add(bowtieIndex)
configDeps += bowtieIndex.jobOutputFile
outputConfig += "bowtie" -> Map("reference_fasta" -> bowtieIndex.reference.getAbsolutePath)
outputConfig += "bowtie" -> Map(
"bowtie_index" -> bowtieIndex.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta"),
"reference_fasta" -> bowtieIndex.reference.getAbsolutePath
)
// Bowtie2 index
val bowtie2Index = new Bowtie2Build(this)
......@@ -116,7 +119,10 @@ class GenerateIndexes(val root: Configurable) extends QScript with BiopetQScript
bowtie2Index.baseName = "reference"
add(bowtie2Index)
configDeps += bowtie2Index.jobOutputFile
outputConfig += "bowtie2" -> Map("reference_fasta" -> bowtie2Index.reference.getAbsolutePath)
outputConfig += "bowtie2" -> Map(
"bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta"),
"reference_fasta" -> bowtie2Index.reference.getAbsolutePath
)
outputConfig += "tophat" -> Map(
"bowtie_index" -> bowtie2Index.reference.getAbsolutePath.stripSuffix(".fa").stripSuffix(".fasta")
)
......
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