mark the example submission rule files as being raw, so the escapes dont get confused

[htsworkflow.git] / encode_submission / encode3.py

diff --git a/encode_submission/encode3.py b/encode_submission/encode3.py
index 875d3bdd9d8205df2eaff65b2b48b5462366645a..53984fc245f460b79a1743fc37eda89187366e6f 100644 (file)
--- a/encode_submission/encode3.py
+++ b/encode_submission/encode3.py
@@ -77,6 +77,12 @@ def main(cmdline=None):
             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:
@@ -85,8 +91,6 @@ def main(cmdline=None):
                                     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:
@@ -111,12 +115,15 @@ def main(cmdline=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:
@@ -182,6 +189,9 @@ def make_parser():
 
     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")