From e4256a921958bf01fbd1eff63e3be6c2737bab6b Mon Sep 17 00:00:00 2001
From: JannikHamp <Jannik.Hamp@mpi-bn.mpg.de>
Date: Mon, 17 Dec 2018 23:04:42 +0100
Subject: [PATCH] $workdir/merged.bed -> "$workdir"/merged.bed

---
 bin/compareBed.sh | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bin/compareBed.sh b/bin/compareBed.sh
index db58a2c..aa2c37e 100644
--- a/bin/compareBed.sh
+++ b/bin/compareBed.sh
@@ -268,7 +268,7 @@ fi
 Rscript --vanilla $path/merge.R $min $max $workdir $data
 
 #5. add fasta sequences to bed and create fasta file
-bedtools getfasta -fi $fasta -bed $workdir/merged.bed -bedOut > $output
+bedtools getfasta -fi $fasta -bed "$workdir"/merged.bed -bedOut > $output
 bedtools getfasta -name -fi $fasta -bed "$output" -fo "$output".fasta
 
 #6 clean up