INDENTED.join(submission_names)))
elif len(submission_names) == 1:
name = submission_names[0]
+
+ if name:
+ submission_uri = get_submission_uri(name)
+ logger.info('Submission URI: %s', name)
+ else:
+ logger.debug('No name, unable to create submission ur')
mapper = None
if opts.make_track_hub:
baseurl=opts.make_track_hub,
baseupload=opts.track_hub_upload,
host=opts.host)
- submission_uri = get_submission_uri(name)
-
if opts.load_rdf is not None:
if submission_uri is None:
flowcells = os.path.join(opts.sequence, 'flowcells')
extractor = CondorFastqExtract(opts.host, flowcells,
model=opts.model,
+ compression=opts.compression,
force=opts.force)
extractor.create_scripts(results)
if opts.scan_submission:
if name is None:
parser.error("Please define a submission name")
+ if mapper is None:
+ parser.error("Scan submission needs --make-track-hub=public-url")
mapper.scan_submission_dirs(results)
if opts.make_track_hub:
parser.add_option('--force', default=False, action="store_true",
help="Force regenerating fastqs")
+ parser.add_option('--compression', default=None, type='choice',
+ choices=['gzip'],
+ help='select compression type for fastq files')
parser.add_option('--daf', default=None, help='specify daf name')
parser.add_option('--library-url', default=None,
help="specify an alternate source for library information")