From 22db60b006ce4abfae2afac238c36f6c7b96f9dc Mon Sep 17 00:00:00 2001
From: Venkat Malladi <venkat.malladi@utsouthwestern.edu>
Date: Sun, 6 Jan 2019 09:16:11 -0600
Subject: [PATCH] Update outdir default.

---
 workflow/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/workflow/main.nf b/workflow/main.nf
index 0332ec6..95a0aea 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
-- 
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