From ef53b1e390a52280b362cd8a62237cd210ff4b71 Mon Sep 17 00:00:00 2001
From: John Garza <johnegarza@wustl.edu>
Date: Mon, 15 Apr 2019 15:27:38 -0500
Subject: [PATCH] Move isn't needed when output prefix is specified

---
 optitype_script.sh | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/optitype_script.sh b/optitype_script.sh
index 66cba9e..5043bd1 100644
--- a/optitype_script.sh
+++ b/optitype_script.sh
@@ -53,6 +53,3 @@ rm -f $TEMPDIR/$name.aln.map.rev.sam
 echo step 5: run Optitype
 # run optitype 
 python /usr/local/bin/OptiType/OptiTypePipeline.py -i $outdir/$name.hla.fwd.fastq $outdir/$name.hla.rev.fastq --dna -v -p $name -o $outdir
-
-#make sure files actually end up in $outdir and not $outdir/<timestamp>, which is where optitype puts them
-mv $outdir/*/* $outdir