From: Diane Trout <diane@caltech.edu>
Date: Tue, 10 Nov 2009 02:06:30 +0000 (+0000)
Subject: Don't add the post_run_command unless the option and a runfolder are specified
X-Git-Tag: 0.4.0~36
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=c0641981d64516a3c158c98f7242a3a29ef50f2e

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 dd60f60..f9d4e3b 100644
--- 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,) ]