detect broken files

.gitlab-ci.yml

@@ -78,6 +78,11 @@ common:setup:
       df -h
       mount
       if [ -n "${RM}" ] ; then rm -rf $RM ; fi
+      for file in find /scratch/snakemake-cache; do
+        if file -b "$file" | grep -E '^ROOT file'; then
+          rootls "$file" 2>/dev/null || echo "$file is broken" 
+        fi
+      done
       find `realpath /scratch` -type l -print0 | (du -sL --files0-from=- || true) | sort -n > /tmp/df
       #find `realpath /scratch` -type f -print0 | du -s --files0-from=- || true | sort -n > /tmp/df
       head /tmp/df