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(from parent 1:
f1e43a8
)
Don't add the post_run_command unless the option and a runfolder are specified
author
Diane Trout
<diane@caltech.edu>
Tue, 10 Nov 2009 02:06:30 +0000
(
02:06
+0000)
committer
Diane Trout
<diane@caltech.edu>
Tue, 10 Nov 2009 02:06:30 +0000
(
02:06
+0000)
htsworkflow/pipelines/retrieve_config.py
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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,) ]