Commit 4585be8d authored by Sander Bollen's avatar Sander Bollen
Browse files

Merge branch 'fix-tophat_unittests' into 'develop'

Fixed tophat unittests

This should fix failing unit tests for tophat

See merge request !220
parents d3473e22 3644ce72
......@@ -267,10 +267,10 @@ class Tophat(val root: Configurable) extends BiopetCommandLineFunction with Refe
override def beforeGraph: Unit = {
super.beforeGraph
if (bowtie1 && !new File(bowtie_index).getParentFile.list().toList
.filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".bt2")))
.filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".ebwt")))
throw new IllegalArgumentException("No bowtie1 index found for tophat")
else if (!new File(bowtie_index).getParentFile.list().toList
.filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".ebwt")))
.filter(_.startsWith(new File(bowtie_index).getName)).exists(_.endsWith(".bt2")))
throw new IllegalArgumentException("No bowtie2 index found for tophat")
}
......
......@@ -142,11 +142,13 @@ object MappingTest {
copyFile("ref.fa")
copyFile("ref.dict")
copyFile("ref.fa.fai")
copyFile("ref.1.bt2")
copyFile("ref.1.ebwt")
val executables = Map(
"reference_fasta" -> (outputDir + File.separator + "ref.fa"),
"db" -> "test",
"bowtie_index" -> "test",
"bowtie_index" -> (outputDir + File.separator + "ref"),
"fastqc" -> Map("exe" -> "test"),
"seqtk" -> Map("exe" -> "test"),
"gsnap" -> Map("exe" -> "test"),
......
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