Add the ability not to build srf files.

This requires that you specify the 'site name' as a flag to turn
on creating the srf files.Add the ability not to build srf files.

diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py
index d628f9bf1623ce20f6fabec3d0206702e2197341..cfa68a4a462d9377e2eefabd1d9c42590a5f66ee 100644 (file)
--- a/htsworkflow/pipelines/runfolder.py
+++ b/htsworkflow/pipelines/runfolder.py
@@ -489,10 +489,11 @@ def extract_results(runs, output_base_dir=None, site="individual", num_jobs=1):
       compress_eland_results(g, cycle_dir)
       
       # build srf commands
-      lanes = range(1,9)
-      run_name = srf.pathname_to_run_name(r.pathname)
-      srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
-      srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
+      if site is not None:
+        lanes = range(1,9)
+        run_name = srf.pathname_to_run_name(r.pathname)
+        srf_cmds = srf.make_commands(run_name, lanes, site, cycle_dir)
+        srf.run_srf_commands(r.bustard.pathname, srf_cmds, 2)
       
 def rm_list(files, dry_run=True):
     for f in files:

diff --git a/scripts/runfolder b/scripts/runfolder
index 2be3ab764589c0d9834dc39c450897469d92c283..76b5dd816b8cfa37a9ff6082dcee312440e6689c 100644 (file)
--- a/scripts/runfolder
+++ b/scripts/runfolder
@@ -70,8 +70,8 @@ def make_parser():
     parser.add_option('--run-xml', dest='run_xml',
            default=None,
            help='specify a run_<FlowCell>.xml file for summary reports')
-    parser.add_option('--site', default='individual',
-                      help='specify the site name for srf files')
+    parser.add_option('--site', default=None,
+                      help='create srf files tagged with the provided site name')
     parser.add_option('-u', '--use-run', dest='use_run', default=None,
                       help='Specify which run to use instead of autoscanning '
                            'the runfolder. You do this by providing the final '