airr-standards

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minimums for physical quantities

2

JSON schema supports defining minimum and maximum values for numbers and integers. As these fields are physical quantities, they should always be positive. Adding these provide for better validation. I...

schristley

Fix ability to capture healthy controls

2

Closes #164 Closes #516

bcorrie

Received the following mail from Read-the-docs today: ---- We are announcing the **deprecation of Sphinx context injection at build time** for all the projects. The deprecation date is set on...

bussec

Does having an actual date for sequencing open the potential for subject identification?

2

My understanding is one technique to avoid subject identification is by replacing dates with relative times from an arbitrary t0 time point and that's what we have done from most...

schristley

Clarification and Reorganization of High-Level Categories in `miairr/data_elements`

1

In the `miairr/data_elements.rst`, we mention having six high-level categories: Study and subject, sample collection, sample processing and sequencing, raw sequences, processing of sequence data, and processed AIRR sequences. However, the...

ustervbo

Addressing Broken Links to Inactive Working Groups

2

In the document `docs/miairr/introduction_miairr.rst`, there's a link to the Minimal Standards Working Group (`http://airr-community.org/working_groups/minimal_standards`). However, this page is currently empty. The AIRR Community WGs page only lists active groups. To...

ustervbo

The `TimePoint` and `TimeQuantity` objects both serve to represent a time value, and only differ slightly in their property names and descriptions. Should we merge these into a single object?

ustervbo

Inconsistency in required elements and properties in `RearrangedSequence` and `UnrearrangedSequence`

3

There appears to be a mismatch in the naming between the required elements and the properties listed in the `RearrangedSequence` and `UnrearrangedSequence` objects. - In `RearrangedSequence`, the `required` list includes...

ustervbo

Update `AIRR Rearrangement TSV Interoperability Example` to use nf-core/airrflow

2

Since a lot of work has gone into the nf-core/airrflow, we could maybe update the chapter 'AIRR Rearrangement TSV Interoperability Example' to this? Maybe Gisela Gabernet can be convinced to...

ustervbo

Combine or restructure the files `guide_miairr_ncbi.rst`, `manual_miairr_ncbi.rst`, `specification_miairr_ncbi.rst`

4

`guide_miairr_ncbi.rst` gives an overview that isn't really reflected in `manual_miairr_ncbi.rst`. For instance, Is Step 2 in `manual_miairr_ncbi.rst` corresponds to step 5 in `guide_miairr_ncbi.rst`, which is described in greater detail in...

ustervbo