rename config file to something that doesn't include the read length

since that has been changing.

also a minor code clean up.

diff --git a/htsworkflow/automation/runner.py b/htsworkflow/automation/runner.py
index 21514c1f18c7c77d9c09f2b64d0212234c37e616..0ab22176b411f71c894fa8d33afa459c65f9191f 100644 (file)
--- a/htsworkflow/automation/runner.py
+++ b/htsworkflow/automation/runner.py
@@ -160,7 +160,7 @@ class Runner(rpc.XmlRpcBot):
 
         # retrieve config step
         cfg_filepath = os.path.join(conf_info.analysis_dir,
-                                    'config32auto.txt')
+                                    'config-auto.txt')
         status_retrieve_cfg = retrieve_config(conf_info,
                                           flowcell,
                                           cfg_filepath,

diff --git a/htsworkflow/pipelines/configure_run.py b/htsworkflow/pipelines/configure_run.py
index 0c1dc8b0ad44bc2d8eb92cf6f27d3f89b73ad609..54677b8ad5cca0879b15a9d6baaf6ab0ac78a7e6 100644 (file)
--- a/htsworkflow/pipelines/configure_run.py
+++ b/htsworkflow/pipelines/configure_run.py
@@ -447,12 +447,11 @@ def configure(conf_info):
   ferr = open(stderr_filepath, 'w')
   
   pipe = subprocess.Popen(['goat_pipeline.py',
-                    '--GERALD=%s' % (conf_info.config_filepath),
-                           #'--tiles=s_4_0100,s_4_0101,s_4_0102,s_4_0103,s_4_0104',
+                           '--GERALD=%s' % (conf_info.config_filepath),
                            '--make',
                            conf_info.analysis_dir],
-                          stdout=fout,
-                          stderr=ferr)
+                           stdout=fout,
+                           stderr=ferr)
 
   print "Configuring pipeline: %s" % (time.ctime())
   error_code = pipe.wait()