From f43b060ee972f73be8ec8ae431c9522c615f354f Mon Sep 17 00:00:00 2001 From: Diane Trout Date: Thu, 8 Oct 2009 00:13:08 +0000 Subject: [PATCH] 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. --- htsworkflow/pipelines/runfolder.py | 9 +++++---- scripts/runfolder | 4 ++-- 2 files changed, 7 insertions(+), 6 deletions(-) diff --git a/htsworkflow/pipelines/runfolder.py b/htsworkflow/pipelines/runfolder.py index d628f9b..cfa68a4 100644 --- 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 2be3ab7..76b5dd8 100644 --- 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_.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 ' -- 2.30.2