$workdir/merged.bed -> "$workdir"/merged.bed

loosolab · Dec 17, 2018 · e4256a9 · e4256a9
1 parent 2b99bb8
commit e4256a9
Showing 1 changed file with 1 addition and 1 deletion.
diff --git 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