Standards Call 2021-11

Agenda

End of year meeting schedule.
Terminology documents (see Call 2021-10, #549).
Follow-up on Travis/Github Actions (#484, #541, #546)
JSON/YAML support: Clean up docs (#547)
Review clonal abundance calculations (#543) and revisit *_count fields (#161).
Follow-up on example Cell schema files (#409): https://gitlab.hzdr.de/scireptor/scireptor_airr_xchange/-/tree/jsonize_add_info/tests/test_data

Next calls: Next call pushed to Mon, 2021-12-06; no call on Mon, 2021-12-27; first call in the new year will be on Mon, 2022-01-24.
Terminology documents: Christian did not have time to work on this, push to next call.
Travis/Github Actions: Timing on Github actions seems okay-ish but hasn't seen a lot of testing. As we still have minutes on Travis, this will be discussed again on the next call.
Cell schema files: Exchange format should be simple; current proposal is a simple implementation; needs demo with 10X; needs to show that conversion into sparse matrix is feasible.
Count field proposal for (#543):
- Rename clone_abundance to clone_count
- Rename sequence_count to umi_count;
- In Clone, we can use duplicate_count for the sum of duplicate_count
- sequence_count, as defined, can be dropped.
JSON/YAML support: Nothing additional to discuss. We just need to clean up the docs.