diff --git a/workflow/main.nf b/workflow/main.nf
index 0332ec64dc402372cf9d8629a08dcb770e8bd925..95a0aea9be9d3bae86b5d66a7ca96ce260f69ba5 100644
--- a/workflow/main.nf
+++ b/workflow/main.nf
@@ -13,7 +13,7 @@ params.bwaIndex = params.genome ? params.genomes[ params.genome ].bwa ?: false :
 params.genomeSize = params.genome ? params.genomes[ params.genome ].genomesize ?: false : false
 params.chromSizes = params.genome ? params.genomes[ params.genome ].chromsizes ?: false : false
 params.cutoffRatio = 1.2
-params.outDir= "$outDir"
+params.outDir= "$baseDir/output"
 params.extendReadsLen = 100
 
 // Check inputs