james hadfield
james hadfield
This issue contains two examples of visualising recombinants. For this issue I've chosen to display BA.1, BA.2, BA.4 and BA.5 as distinct recombinants, however that choice is clearly up for...
This introduces a script which restricts the 6m builds to include tips from the previous 6 months only. This is done _after_ tree building, so that tree reconstruction / inference...
This PR adds an example which produces an omicron-only build. Viewable here: https://nextstrain.org/staging/ncov/omicron/2022-04-20  To do this we have to modify the rules and add an extra (optional) parameter `config["files"]["include_for_subsampling"]`...
## Description of proposed changes This implements subsampling via a single script, rather than a series of snakemake commands. The behavior is intended to be the same, and the the...
**Context** Many scripts need to check if a value is "valid" before proceeding. These checks tend to be one-offs and therefore slightly different. This makes it hard to document /...
Once Augur PR https://github.com/nextstrain/augur/pull/728 as been merged & this repo updated to use the new version of Augur we can simplify the workflow as follows: * The `main_workflow.smk` can be...
A common source of errors is missing / improperly formatted metadata fields (e.g. [this](https://discussion.nextstrain.org/t/error-in-main-workflow-smk-file-in-latency-wait/616/2)). These often result in stack traces rather than helpful error messages. We [document](https://github.com/nextstrain/ncov/blob/master/docs/metadata-fields.md) the "standard" metadata...
This workflow was originally implemented as part of #668, but I've split it into a separate PR to debug the failing tests. (Note that tests pass locally on my machine.)...
This commit is a WIP commit to test the new functionality being introduced in augur PR 728 [1]. This allows us to simplify the nCoV workflow as we can explicitly...
During development of #628 (which is not yet merged) we duplicated a sizeable amount of the build configuration. This issue serves as a reminder to reduce this duplication, where it...