Automatically add the flowcell subdirectory to the sequence archive path

[htsworkflow.git] / encode_submission / geo_gather.py

diff --git a/encode_submission/geo_gather.py b/encode_submission/geo_gather.py
index 9a1f51e7564431a28cf1f5b99b2b38f74574f739..a2901058371ecec871224076f94362a3eaf6ce43 100644 (file)
--- a/encode_submission/geo_gather.py
+++ b/encode_submission/geo_gather.py
@@ -77,7 +77,8 @@ def main(cmdline=None):
         results.make_tree_from(opts.make_tree_from)
 
     if opts.fastq:
-        extractor = CondorFastqExtract(opts.host, apidata, opts.sequence,
+        flowcells = os.path.join(opts.sequence, 'flowcells')
+        extractor = CondorFastqExtract(opts.host, flowcells,
                                        force=opts.force)
         extractor.create_scripts(results)