Add building srf files to runfolder as part of --extract-results

[htsworkflow.git] / scripts / runfolder

diff --git a/scripts/runfolder b/scripts/runfolder
index 1380fbf7fde7affcd856d2884af1889811ba3fe2..2be3ab764589c0d9834dc39c450897469d92c283 100644 (file)
--- a/scripts/runfolder
+++ b/scripts/runfolder
@@ -56,26 +56,28 @@ def make_parser():
                         help='generate run configuration archive')
     commands.add_option('--extract-results', action='store_true',
            default=False,
-           help='create run-xml summary, compress the eland result files, and '
-                'copy them and the Summary.htm file into archival directory.')
+           help='create run-xml summary, compress the eland result files, build srf files and '
+                'copy all that and the Summary.htm file into an archival directory.')
     commands.add_option('-c', '--clean', action='store_true', default=False,
                         help='Clean runfolder, preparing it for long-term storage')
     parser.add_option_group(commands)
 
+    parser.add_option('-j', '--max-jobs', default=1,
+                      help='sepcify the maximum number of processes to run '
+                           '(used in extract-results)')
     parser.add_option('-o', '--output-dir', default=None,
            help="specify the default output directory for extract results")
-
+    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('-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 '
                            ' GERALD directory, and it assumes the parent '
                            'directories are the bustard and image processing '
                            'directories.')
-                    
-    parser.add_option('--run-xml', dest='run_xml',
-           default=None,
-           help='specify a run_<FlowCell>.xml file for summary reports')
-    
 
     return parser
 
@@ -119,7 +121,7 @@ def main(cmdlist=None):
             runfolder.extract_run_parameters(runs)
             command_run = True
         if opt.extract_results:
-            runfolder.extract_results(runs, opt.output_dir)
+            runfolder.extract_results(runs, opt.output_dir, opt.site, opt.max_jobs)
             command_run = True
         if opt.clean:
             runfolder.clean_runs(runs, opt.dry_run)