list offending directories

.gitlab-ci.yml

@@ -93,6 +93,7 @@ common:setup:
               print(filename)
       EOF
       :>list
+      if [ -n "${REPAIR}" ]; then
         for file in $(find /scratch/snakemake-cache -type f); do
           if file -b "$file" | grep -E '^ROOT file' >/dev/null; then
             echo "$file" > list
@@ -100,10 +101,13 @@ common:setup:
         done
         cat list | python filter_broken.py | tee broken
         cat broken | xargs --no-run-if-empty rm -v
+      fi
       echo "removing broken symlinks"
       find `realpath /scratch` -xtype l -print -delete
-      echo "listing cached entries by size"
-      find `realpath /scratch` -type l -print0 | (du -sL --files0-from=- || true) | sort -n > /tmp/df
+      echo "listing most offending directories"
+      find `realpath /scratch` -type d -print0 | (du -sL --files0-from=- || true) | sort -n > /tmp/df
+      #echo "listing cached entries by size"
+      #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
       tail -n 1000 /tmp/df