diff --git a/.github/workflows/linux.yml b/.github/workflows/linux.yml
index 599b0e3c53..ce0052f78d 100644
--- a/.github/workflows/linux.yml
+++ b/.github/workflows/linux.yml
@@ -30,6 +30,7 @@ jobs:
           git config --global user.name "ciuser" && \
           git config --global user.email "ci@openquantumsafe.org" && \
           export LIBOQS_DIR=`pwd` && \
+          git config --global --add safe.directory $LIBOQS_DIR && \
           cd scripts/copy_from_upstream && \
           ! pip3 install -r requirements.txt 2>&1 | grep ERROR && \
           python3 copy_from_upstream.py copy && \
diff --git a/scripts/copy_from_upstream/copy_from_upstream.py b/scripts/copy_from_upstream/copy_from_upstream.py
index 99d04c6347..92264fb1bb 100755
--- a/scripts/copy_from_upstream/copy_from_upstream.py
+++ b/scripts/copy_from_upstream/copy_from_upstream.py
@@ -611,8 +611,6 @@ def copy_from_upstream():
     for t in ["kem", "sig"]:
         with open(os.path.join(os.environ['LIBOQS_DIR'], 'tests', 'KATs', t, 'kats.json'), "w") as f:
             json.dump(kats[t], f, indent=2, sort_keys=True)
-    if not keepdata:
-        shutil.rmtree('repos')
 
     update_upstream_alg_docs.do_it(os.environ['LIBOQS_DIR'])
 
@@ -622,6 +620,10 @@ def copy_from_upstream():
     update_docs_from_yaml.do_it(os.environ['LIBOQS_DIR'])
     update_cbom.update_cbom_if_algs_not_changed(os.environ['LIBOQS_DIR'], "git")
 
+    if not keepdata:
+        shutil.rmtree('repos')
+
+
 def verify_from_upstream():
     instructions = load_instructions()
     basedir = "verify_from_upstream"