Don't add the post_run_command unless the option and a runfolder are specified

diff --git a/htsworkflow/pipelines/retrieve_config.py b/htsworkflow/pipelines/retrieve_config.py
index dd60f6090188ab59260242de9c2a5b69014d1eae..f9d4e3ba0df83a4b918a5fafcdc5e5cded75c117 100644 (file)
--- a/htsworkflow/pipelines/retrieve_config.py
+++ b/htsworkflow/pipelines/retrieve_config.py
@@ -148,7 +148,7 @@ def format_gerald_config(options, flowcell_info, genome_map):
         config += ['%s:USE_BASES Y%s' % ( lane_prefix, read_length ) ]
 
     # add in option for running script after 
-    if options.post_run is not None:
+    if not (options.post_run is None or options.runfolder is None):
         runfolder = os.path.abspath(options.runfolder)
         post_run = options.post_run  % {'runfolder': runfolder}
         config += ['POST_RUN_COMMAND %s' % (post_run,) ]