mpoelchau
commented
4 years ago Update to clarify the problem:
- add-bw-track_gaps and add-bw-track_gc need a different --bw_url entry. It should include the prefix 'bigwig/' (since that's the directory they'll live in)
- add_metadata - the metadata for the gap and gc bigwig tracks is not in the final trackList.json file
It looks like the following steps in flow_apollo2 are silently failing - they exit with a success message, but they don't actually edit the information in trackList.json - or perhaps they are but the edited file isn't propagated in flow_dispatch. Hard to say.
add-bw-track_gaps add-bw-track_gc add_metadata