diff --git a/sisyphus/global_settings.py b/sisyphus/global_settings.py
index 5709c49..498aa37 100644
--- a/sisyphus/global_settings.py
+++ b/sisyphus/global_settings.py
@@ -130,8 +130,10 @@ def file_caching(path):
 JOB_CLEANER_INTERVAL = 60
 #: How many threads should be cleaning in parallel
 JOB_CLEANER_WORKER = 5
-#: If the job internal work directory should be keeped re deleted during clean up
+#: If the job internal work directory should be kept or deleted during clean up
 JOB_CLEANUP_KEEP_WORK = False
+#: If the job internal input directory with symlinks to input jobs should be kept or deleted during clean up
+JOB_CLEANUP_KEEP_INPUT = False
 #: Default value for job used by tk.cleaner to determine if a job should be removed or not
 JOB_DEFAULT_KEEP_VALUE = 50
 #: How many threads should update the graph in parallel, useful if the filesystem has a high latency
diff --git a/sisyphus/job.py b/sisyphus/job.py
index d016d6e..b2a3b53 100644
--- a/sisyphus/job.py
+++ b/sisyphus/job.py
@@ -516,10 +516,12 @@ def _sis_cleanup(self):
                 try:
                     if not gs.JOB_CLEANUP_KEEP_WORK:
                         shutil.rmtree(os.path.abspath(self._sis_path(gs.JOB_WORK_DIR)))
+                    if not gs.JOB_CLEANUP_KEEP_INPUT:
+                        shutil.rmtree(os.path.abspath(self._sis_path(gs.JOB_INPUT)))
                     files = [
                         i
                         for i in os.listdir(self._sis_path())
-                        if i not in (gs.JOB_OUTPUT, gs.JOB_INFO, gs.JOB_WORK_DIR)
+                        if i not in (gs.JOB_OUTPUT, gs.JOB_INFO, gs.JOB_WORK_DIR, gs.JOB_INPUT)
                     ]
                     subprocess.check_call(
                         ["tar", "-czf", gs.JOB_FINISHED_ARCHIVE] + files, cwd=os.path.abspath(self._sis_path())