Current status of the discussion on Germline/Genotype
representation in the Schema (#530).
Review clonal abundance calculations (#543) and revisit
*_count fields (#161).
DataProcessing sprint is done, need to turn the discussion and
results into action items and Github issues.
Minutes
Meta
Date: Mon, 2021-10-04 18:00 UTC
Present: Brian, Felix, Jason, Kira, Christian, Francisco, Susanna, Scott
Regrets: Chaim
Topics
Travis/Github Actions: R-CMD is running both on Travis and Github
Actions now. Both take around 4 min for a complete run, but Actions
do use dependence (i.e., only test if something was changed). Also,
Github Actions seems to have better integration into Github and would
provide us with twice as many credits/minutes, at apparently equal
execution speed. Jason will run one more performance comparison
between the two and look at conditional testing for Travis.
CellProperty implementation:
Every property will have one (locally) unique feature_id
(which is rather a label than an ID). Additional PIDs for a
feature_id might be included as:
additional keys in the JSON
normalized representation in a relational DB backend
additional files for a matrix TSV, as defined by AnnData.
We agreed that the TSV and the JSON may look structurally
different, i.e., TSV being a matrix (one row per cell) while the
JSON being an normalized hash-of-hashes.
Normalization (division operation, not the data representation)
is useful when data is queried in a repository, but people will
usually want to download non-normlized data, to apply their own
routines. This might ultimately require the storage of at least
two levels of the same data (i.e., two matrices).
To keep moving, we will only support a single feature_id for
now, but keep a future extension of feature IDs/labels open. The
API will deliver JSON-formated data, which will be identical to
the on-disk JSON file. The TSV will be plain matrix with a column
header and a cell_id index column. This will be potentially
expanded with further AnnData files.
JSON/YAML support: Brian will work on the docs, will continue next
call.
Terminology documents: Agreement that there should be only one
document, but it may exist on both RTD and Zenodo. Will need to
discuss the hierarchy of the two platforms next time.
*_count fields: Pushed to next call, but will have priority then,
as SFU team would like to come to a closure regarding clone counts
(#543) and the various rearrangement counts (#161) are closely
linked. Therefore please comment on these issues soon.