From 43e9067c36e5118313066bd2a7b20dc9fb454601 Mon Sep 17 00:00:00 2001
From: Mengjia Lyu <53891017+YumekaMengjiaLYU@users.noreply.github.com>
Date: Mon, 20 Sep 2021 11:47:55 -0400
Subject: [PATCH] Update bootstrap-qsiprep.sh

modified the -w directory in singularity run of qsiprep_zip.sh
---
 scripts/cubic/bootstrap-qsiprep.sh | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/scripts/cubic/bootstrap-qsiprep.sh b/scripts/cubic/bootstrap-qsiprep.sh
index 87c277b..7f96e32 100644
--- a/scripts/cubic/bootstrap-qsiprep.sh
+++ b/scripts/cubic/bootstrap-qsiprep.sh
@@ -217,14 +217,14 @@ set -e -u -x
 
 subid="$1"
 
-mkdir -p ${PWD}/.git/tmp/wdir
+mkdir -p ${PWD}/.git/tmp/wkdir
 singularity run --cleanenv -B ${PWD} \
     pennlinc-containers/.datalad/environments/qsiprep-0-14-2/image \
     inputs/data \
     prep \
     participant \
     -v -v \
-    -w ${PWD}/.git/wkdir \
+    -w ${PWD}/.git/tmp/wkdir \
     --n_cpus $NSLOTS \
     --stop-on-first-crash \
     --fs-license-file code/license.txt \